The Quran commands Muslims to fight all unbelievers:
Fight those who believe not in God nor the Last Day, nor hold that forbidden which hath been forbidden by God and His Apostle, nor acknowledge the religion of Truth, (even if they are) of the People of the Book, until they pay the Jizya with willing submission, and feel themselves subdued. S. 9:29
The above emphatically exhorts Muslims to conquer the following groups of people until they pay a sum of money (Jizya) as a sign of their subjection and humiliation:
Atheists/Agnostics (those who believe not in God nor the Last Day).
Jews and Christians (people of the Book).
Everyone else, whether Hindus/ Magians, Buddhists etc., since these groups do not prohibit what Muhammad forbade nor believe in Islam, the so-called "religion of Truth".
Please note that the passage does not limit the taking of Jizya from the Jews and Christians; it clearly says that the Jizya is to be extracted from all of the subjugated groups that are listed, i.e. those who do not believe in Allah and the last day, or forbid what Muhammad forbade etc.
To say, as some try do, that this verse is referring only to the Jews and Christians makes absolutely no sense when we note that these groups believe in Allah and the last day, just as the Quran testifies:
And dispute ye not with the People of the Book, except with means better (than mere disputation), unless it be with those of them who inflict wrong (and injury): but say, "We believe in the revelation which has come down to us and in that which came down to you; Our God and your God is one; and it is to Him we bow (in Islam)." S. 29:46
Those who believe (in the Qur'an), those who follow the Jewish (scriptures), and the Sabians and the Christians, - any who believe in God and the Last Day, and work righteousness, - on them shall be no fear, nor shall they grieve. S. 5:69, cf. 2:62
This last reference presupposes that Jews and Christians are among those who believe in Allah and the last day. How, then, can the Jews and Christians be listed with those who do not believe in the existence of God and the final judgment? Doesn’t this make it rather obvious that the Quran has some other group in view besides the Jews and Christians from whom Jizya can be extracted?
This, perhaps, explains why Muslim leaders such as Umar ibn al-Khattab took Jizya from the Persians even though they were labeled pagans, specifically al-mushrikeen or those who ascribe partners with Allah:
Narrated Jubair bin Haiya:
'Umar sent the Muslims to the great countries to fight the pagans. When Al-Hurmuzan embraced Islam, 'Umar said to him, "I would like to consult you regarding these countries which I intend to invade." Al-Hurmuzan said, "Yes, the example of these countries and their inhabitants who are the enemies of the Muslims, is like a bird with a head, two wings and two legs; If one of its wings got broken, it would get up over its two legs, with one wing and the head; and if the other wing got broken, it would get up with two legs and a head, but if its head got destroyed, then the two legs, two wings and the head would become useless. The head stands for Khosrau, and one wing stands for Caesar and the other wing stands for Faris. So, order the Muslims to go towards Khosrau." So, 'Umar sent us (to Khosrau) appointing An-Nu’man bin Muqrin as our commander. When we reached the land of the enemy, the representative of Khosrau came out with forty-thousand warriors, and an interpreter got up saying, "Let one of you talk to me!" Al-Mughira replied, "Ask whatever you wish." The other asked, "Who are you?" Al-Mughira replied, "We are some people from the Arabs; we led a hard, miserable, disastrous life: we used to suck the hides and the date stones from hunger; we used to wear clothes made up of fur of camels and hair of goats, and to worship trees and stones. While we were in this state, the Lord of the Heavens and the Earths, Elevated is His Remembrance and Majestic is His Highness, sent to us from among ourselves a Prophet whose father and mother are known to us. Our Prophet, the Messenger of our Lord, has ordered us to fight you till you worship Allah Alone or give Jizya (i.e. tribute); and our Prophet has informed us that our Lord says:-- "Whoever amongst us is killed (i.e. martyred), shall go to Paradise to lead such a luxurious life as he has never seen, and whoever amongst us remain alive, shall become your master." (Al-Mughira, then blamed An-Nu’man for delaying the attack and) An-Nu'man said to Al-Mughira, "If you had participated in a similar battle, in the company of Allah's Apostle he would not have blamed you for waiting, nor would he have disgraced you. But I accompanied Allah’s Apostle in many battles and it was his custom that if he did not fight early by daytime, he would wait till the wind had started blowing and the time for the prayer was due (i.e. after midday)." (Sahih al-Bukhari, Volume 4, Book 53, Number 386)
Now lest a Muslim say that the Persians were also classified as being from the people of the book note the following text:
And this is a Book which We have revealed as a blessing: so follow it and be righteous, that ye may receive mercy: Lest ye should say: "The Book was sent down to two Peoples before us, and for our part, we remained unacquainted with all that they learned by assiduous study:" S. 6:155-156
The two peoples mentioned here are the Jews and Christians:
(Lest ye should say) so that you will not say, O people of Mecca, on the Day of Judgement: (The Scripture was revealed only to two sects) the people of two religions (before us) i.e. the Jews and Christians, (and we in sooth were unaware) ignorant (of what they read) their reading of the Torah and the Gospel; (Tanwîr al-Miqbâs min Tafsîr Ibn ‘Abbâs; source)
We have revealed it, lest you should say, 'The Scripture was revealed only upon two parties - the Jews and the Christians - before us and we (in has been softened, its noun omitted, in other words [read as] inna) indeed have been unacquainted with their study', their reading [of the scripture], not knowing any of it, since it is not in our own language. (Tafsir al-Jalalayn; source)
Clearly, the Quran doesn’t include anyone other than the Jews and Christians as the people of the book since they were the only ones who were given the book from Allah. Therefore, if the Quran were limiting the taking of Jizya to the people of the book then Muhammad violated the orders of his own scripture by permitting the Persians to pay it since they are not part of this group.
In fact, Muhammad himself is reported to have permitted his followers to take Jizya from the pagans/polytheists:
Chapter 2: APPOINTMENT OF THE LEADERS OF EXPEDITIONS BY THE IMAM AND HIS ADVICE TO THEM ON ETIQUETTES OF WAR AND RELATED MATTERS
It has been reported from Sulaiman b. Buraid through his father that when the Messenger of Allah (may peace be upon him) appointed anyone as leader of an army or detachment he would especially exhort him to fear Allah and to be good to the Muslims who were with him. He would say: Fight in the name of Allah and in the way of Allah. Fight against those who disbelieve in Allah. Make a holy war, do not embezzle the spoils; do not break your pledge; and do not mutilate (the dead) bodies; do not kill the children. When you meet your enemies who are polytheists, invite them to three courses of action. If they respond to any one of these, you also accept it and withhold yourself from doing them any harm. Invite them to (accept) Islam; if they respond to you, accept it from them and desist from fighting against them. Then invite them to migrate from their lands to the land of Muhajirs and inform them that, if they do so, they shall have all the privileges and obligations of the Muhajirs. If they refuse to migrate, tell them that they will have the status of Bedouin Muslims and will be subjected to the Commands of Allah like other Muslims, but they will not get any share from the spoils of war or Fai' except when they actually fight with the Muslims (against the disbelievers). If they refuse to accept Islam, demand from them the Jizya. If they agree to pay, accept it from them and hold off your hands. If they refuse to pay the tax, seek Allah’s help and fight them. When you lay siege to a fort and the besieged appeal to you for protection in the name of Allah and His Prophet, do not accord to them the guarantee of Allah and His Prophet, but accord to them your own guarantee and the guarantee of your companions for it is a lesser sin that the security given by you or your companions be disregarded than that the security granted in the name of Allah and His Prophet be violated. When you besiege a fort and the besieged want you to let them out in accordance with Allah’s Command, do not let them come out in accordance with His Command, but do so at your (own) command, for you do not know whether or not you will be able to carry out Allah’s behest with regard to them. (Sahih Muslim, Book 019, Number 4294)
All of this presupposes that Islam permits the existence of other religions and worldviews under its umbrella, provided that those who embrace such beliefs are willing to pay Jizya.
This may account for why the following Muslim scholar believed that Q. 9:29 refers to all disbelieving groups, not just to Jews and Christians:
Verse 28 appearing earlier referred to Jihad against the Mushriks of Makkah. The present verses talk about Jihad against the People of the Book. In a sense, this is a prelude to the battle of Tabuk that was fought against the People of the Book. In Tafsir al-Durr al-Manthur, it has been reported from the Quran commentator, Mujahid that these verses have been revealed about the battle of Tabuk. Then, there is the reference to ‘those who were given the Book’. In Islamic religious terminology, they are referred to as ‘ahl al-Kitab’ or People of the Book. In its literal sense, it covers every disbelieving group of people who believe in a Scripture but, in the terminology of the Holy Quran, this term is used for Jews and Christians only - because, only these two groups from the People of the Book were well-known in and around Arabia. Therefore, addressing the Mushriks of Arabia, the Holy Quran has said…
lest you should say, "The Book was sent down only upon two groups before us, were ignorant of what they studied." – 6:156
As for the injunction of Jihad against the People of the Book given in verse 29, it is really not particular to the People of the Book. The fact is that this very injunction applies to all disbelieving groups - because, the reasons for the injunction to fight mentioned next are common to all disbelievers. If so, the injunction has to be common too. But, the People of the Book were mentioned here particularly to serve a purpose…
Regarding the instruction given in this verse that once these people have agreed to pay jizyah, fighting should be stopped, a little explanation may be useful. According to the majority of Muslim jurists, it includes all disbelievers – whether from the People of the Book or from those other than them. However, the Mushriks of Arabia stand excluded from it for jizyah was not accepted from them. (Mufti Shafi Usmani, Maariful Quran, Volume 4, pp. 360-361, 365; source; bold and underline emphasis ours)
But this contradicts other passages of the Quran, as well as specific Islamic narratives, which demand that those who claim that Allah has a son or that he has co-equal partners must convert to Islam or die:
And an announcement from God and His Apostle, to the people (assembled) on the day of the Great Pilgrimage,- that God and His Apostle dissolve (treaty) obligations with the Pagans (al-mushrikeen- literally, those who associate partners with God). If then, ye repent, it were best for you; but if ye turn away, know ye that ye cannot frustrate God. And proclaim a grievous penalty to those who reject Faith. (But the treaties are) not dissolved with those Pagans (al-mushrikeen) with whom ye have entered into alliance and who have not subsequently failed you in aught, nor aided any one against you. So fulfil your engagements with them to the end of their term: for God loveth the righteous. But when the forbidden months are past, then fight and slay the Pagans (al-mushrikeen) wherever ye find them, an seize them, beleaguer them, and lie in wait for them in every stratagem (of war); but if they repent, and establish regular prayers and practise regular charity, then open the way for them: for God is Oft-forgiving, Most Merciful. If one amongst the Pagans (al-mushrikeen) ask thee for asylum, grant it to him, so that he may hear the word of God; and then escort him to where he can be secure. That is because they are men without knowledge… O ye who believe! Truly the Pagans (al-mushrikoon) are unclean; so let them not, after this year of theirs, approach the Sacred Mosque. And if ye fear poverty, soon will God enrich you, if He wills, out of His bounty, for God is All-knowing, All-wise… The Jews call 'Uzair a son of God, and the Christians call Christ the son of God. That is a saying from their mouth; (in this) they but imitate what the unbelievers of old used to say. God's curse be on them: how they are deluded away from the Truth! They take their priests and their anchorites to be their lords in derogation of God, and (they take as their Lord) Christ the son of Mary; yet they were commanded to worship but One God: there is no god but He. Praise and glory to Him: (Far is He) from having the partners they associate (yushrikoon) (with Him). Fain would they extinguish God's light with their mouths, but God will not allow but that His light should be perfected, even though the Unbelievers may detest (it). It is He Who hath sent His Apostle with guidance and the Religion of Truth, to proclaim it over all religion, even though the Pagans may detest (it). S. 9:3-6, 28, 30-33
The foregoing plainly states that:
Muslims must fight and slay al-mushrikeen wherever they find them unless they repent and convert to Islam.
Al-mushrikeen are unclean and therefore cannot approach the sacred mosque, that is the Kaba in Mecca.
Jews and Christians are al-mushrikeen because they ascribe partners with God, i.e. Jews believe that Ezra is God’s son and that their rabbis are lords besides God, whereas the Christians profess that Jesus is the Son of God and that he and the Christian monks are lords in place of God.
What this basically implies is that Muslims must fight and slay the Jews and Christians until they repent and become Muslims. The hadith literature provides substantiation for our exegesis since it quotes Muhammad as saying that he was ordered to fight the people, not just the Meccans, until they become Muslims:
Narrated Ibn ‘Umar:
Allah's Apostle said: "I have been ordered (by Allah) to fight against the people until they testify that none has the right to be worshipped but Allah and that Muhammad is Allah's Apostle, and offer the prayers perfectly and give the obligatory charity, so if they perform a that, then they save their lives an property from me except for Islamic laws and then their reckoning (accounts) will be done by Allah." (Sahih al-Bukhari, Volume 1, Book 2, Number 24)
Narrated Anas bin Malik:
Allah's Apostle said, "I have been ordered to fight the people till they say: ‘None has the right to be worshipped but Allah.’ And if they say so, pray like our prayers, face our Qibla and slaughter as we slaughter, then their blood and property will be sacred to us and we will not interfere with them except legally and their reckoning will be with Allah." Narrated Maimun ibn Siyah that he asked Anas bin Malik, "O Abu Hamza! What makes the life and property of a person sacred?" He replied, "Whoever says, ‘None has the right to be worshipped but Allah’, faces our Qibla during the prayers, prays like us and eats our slaughtered animal, then he is a Muslim, and has got the same rights and obligations as other Muslims have." (Sahih al-Bukhari, Volume 1, Book 8, Number 387)
Chapter 9: COMMAND FOR FIGHTING AGAINST THE PEOPLE SO LONG AS THEY DO NOT PROFESS THAT THERE IS NO GOD BUT ALLAH AND MUHAMMAD IS HIS MESSENGER
It is narrated on the authority of Abu Huraira that when the Messenger of Allah (may peace be upon him) breathed his last and Abu Bakr was appointed as his successor (Caliph), those amongst the Arabs who wanted to become apostates became apostates. 'Umar b. Khattab said to Abu Bakr: Why would you fight against the people, when the Messenger of Allah declared: I have been directed to fight against people so long as they do not say: There is no god but Allah, and he who professed it was granted full protection of his property and life on my behalf except for a right? His (other) affairs rest with Allah. Upon this Abu Bakr said: By Allah, I would definitely fight against him who severed prayer from Zakat, for it is the obligation upon the rich. By Allah, I would fight against them even to secure the cord (used for hobbling the feet of a camel) which they used to give to the Messenger of Allah (as zakat) but now they have withheld it. Umar b. Khattab remarked: By Allah, I found nothing but the fact that Allah had opened the heart of Abu Bakr for (perceiving the justification of) fighting (against those who refused to pay Zakat) and I fully recognized that the (stand of Abu Bakr) was right. (Sahih Muslim, Book 001, Number 0029)
It is reported on the authority of Abu Huraira that the Messenger of Allah said: I have been commanded to fight against people so long as they do not declare that there is no god but Allah, and he who professed it was guaranteed the protection of his property and life on my behalf except for the right affairs rest with Allah. (Sahih Muslim, Book 001, Number 0030)
It is narrated on the authority of Jabir that the Messenger of Allah said: I have been commanded that I should fight against people till they declare that there is no god but Allah, and when they profess it that there is no god but Allah, their blood and riches are guaranteed protection on my behalf except where it is justified by law, and their affairs rest with Allah, and then he (the Holy Prophet) recited (this verse of the Holy Qur'an): "Thou art not over them a warden" (lxxxviii, 22). (Sahih Muslim, Book 001, Number 0032)
It has been narrated on the authority of Abdullah b. 'Umar that the Messenger of Allah said: I have been commanded to fight against people till they testify that there is no god but Allah, that Muhammad is the messenger of Allah, and they establish prayer, and pay Zakat and if they do it, their blood and property are guaranteed protection on my behalf except when justified by law, and their affairs rest with Allah. (Sahih Muslim, Book 001, Number 0033)
And he (peace and blessings of Allaah be upon him) said: "I have been sent just before the Hour with the sword, so that Allaah will be worshipped ALONE with no partner or associate." Narrated by Ahmad, 4869; classed as saheeh by al-Albaani in Saheeh al-Jaami', 2831. (Question No. 34647: The reason why jihaad is prescribed; source; capital and underline emphasis ours)
Thus, even Jews and Christians, not just the Arab pagans, had to convert to Islam otherwise Muslims would have to kill them as well if they didn’t.
This further implies that Jews and Christians could not approach Mecca since, being al-mushrikeen, they are unclean. We again find the hadiths substantiating this very point:
Narrated Ibn 'Umar:
Umar expelled the Jews and the Christians from Hijaz. When Allah's Apostle had conquered Khaibar, he wanted to expel the Jews from it as its land became the property of Allah, His Apostle, and the Muslims. Allah's Apostle intended to expel the Jews but they requested him to let them stay there on the condition that they would do the labor and get half of the fruits. Allah’s Apostle told them, "We will let you stay on thus condition, as long as we wish." So, they (i.e. Jews) kept on living there until 'Umar forced them to go towards Taima' and Ariha'. (Sahih al-Bukhari, Volume 3, Book 39, Number 531)
It has been narrated by 'Umar b. al-Khattab that he heard the Messenger of Allah (may peace be upon him) say: I will expel the Jews and Christians from the Arabian Peninsula and will not leave any but Muslim. (Sahih Muslim, Book 019, Number 4366)
To summarize the contradictions:
Q. 9:29 along with certain Islamic narrations teach that Muslims are to fight all the unbelievers until they pay the Jizya and feel subdued. This presupposes that Islam allows even pagans to live under Muslim rule without having to convert to the Islamic faith.
Q. 9:1-6, 28, 30-33 all say that Muslims are to kill those who associate other beings with God, including Jews and Christians, until they repent and become Muslims. The hadith literature provides attestation that this is precisely what Muhammad commanded, specifically, that he (and subsequently his followers) was to fight all the people until they became Muslims. This naturally assumes that Jews and Christians, not just the pagans, must convert to the Islamic faith or die.
There is a way in which Muslims can reconcile Q. 9:29 with what immediately precedes and follows. One can understand from Sura 9 that all those who convert to Islam, whether pagans, Jews, Christians etc., are to pay Jizya as a sign that they have been subdued and brought into the fold of Islam.
Although this may solve the contradiction within the Quran it doesn’t help resolve the problems raised by the hadith literature. The Islamic narratives quote Muhammad as expressly stating that the people must be fought until they testify that Allah is god and that he is his messenger which not only contradicts the Quran but also conflicts with the other reports that we quoted where Muslims allowed pagans such as the Persians to remain in their religion provided that they paid Jizya.
Hence, no matter how a Muslim tries to reconcile all of this some of the contradictions will still remain.
All Quranic citations were taken from the Abdullah Yusuf Ali version.