Ibn Kathir, likely the Muslim world's most respected Quran commentator, says Allah's pardon of the unbelievers was canceled by Quran Chapter 9 and its verses of the sword

Kathir explains here (if you go there, scroll down to the bottom third of the page) that Quran 2:109, which he quotes without giving its chapter and verse number, and which advises Muslims to be tolerant toward unbelievers, has been canceled by verses in Quran Chapter 9 (which Muslim scholars generally agree was one of the last Quran chapters revealed). Kathir quotes part of Quran 9:5, but here's the whole verse:

Then, when the sacred months have passed, slay the idolaters wherever ye find them, and take them (captive), and besiege them, and prepare for them each ambush. But if they repent and establish worship and pay the poor-due, then leave their way free. Lo! Allah is Forgiving, Merciful.

And Kathir quotes part of Quran 9:29. Again, here's the whole verse:

Fight those who do not believe in Allah, nor in the latter day, nor do they prohibit what Allah and His Messenger [Muhammad] have prohibited, nor follow the religion of truth [Islam], out of those who have been given the Book [the Bible, given to Christian and Jews], until they pay the tax in acknowledgment of [Muslim] superiority and they are in a state of subjection [this subjection is a source of Islamic law's institution of dhimmitude, i.e., third-class legal status for non-Muslims].

Notice that 9:29 does not say "fight in self-defense." It says "fight those who do not believe" in Islam.

Anyway, then Kathir says,

Allah's pardon for the disbelievers was repealed. Abu Al-`Aliyah, Ar-Rabi` bin Anas, Qatadah and As-Suddi said similarly: "It [the pardon, or forgiveness] was abrogated by the Ayah [verse] of the sword." [The verse of the sword is Qur'an 9:5 ]