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You have to bring out the examples of tolerance in their scripture.

There is a structure to the Qur'an. Later parts supercede earlier parts. The order that Muhammad dictated the surahs is not the order they are placed in the Qur'an. References to tolerance are from the early part when Muhammad was weak. Surah 9 is actually the 113th and next-to-last "revealed" in which peace with non-Muslims is repudiated and perpetual war declared.

[9.1] (This is a declaration of) immunity by Allah and His Apostle towards those of the idolaters with whom you made an agreement.
[9.2] So go about in the land for four months and know that you cannot weaken Allah and that Allah will bring disgrace to the unbelievers.
[9.3] And an announcement from Allah and His Apostle to the people on the day of the greater pilgrimage that Allah and His Apostle are free from liability to the idolaters; therefore if you repent, it will be better for you, and if you turn back, then know that you will not weaken Allah; and announce painful punishment to those who disbelieve.
[9.4] Except those of the idolaters with whom you made an agreement, then they have not failed you in anything and have not backed up any one against you, so fulfill their agreement to the end of their term; surely Allah loves those who are careful (of their duty).
[9.5] So when the sacred months have passed away, then slay the idolaters wherever you find them, and take them captives and besiege them and lie in wait for them in every ambush, then if they repent and keep up prayer and pay the poor-rate, leave their way free to them; surely Allah is Forgiving, Merciful.
[9.6] And if one of the idolaters seek protection from you, grant him protection till he hears the word of Allah, then make him attain his place of safety; this is because they are a people who do not know.
[9.7] How can there be an agreement for the idolaters with Allah and with His Apostle; except those with whom you made an agreement at the Sacred Mosque? So as long as they are true to you, be true to them; surely Allah loves those who are careful (of their duty).
[9.8] How (can it be)! while if they prevail against you, they would not pay regard in your case to ties of relationship, nor those of covenant; they please you with their mouths while their hearts do not consent; and most of them are transgressors.
[9.9] They have taken a small price for the communications of Allah, so they turn away from His way; surely evil is it that they do.
[9.10] They do not pay regard to ties of relationship nor those of covenant in the case of a believer; and these are they who go beyond the limits.
[9.11] But if they repent and keep up prayer and pay the poor-rate, they are your brethren in faith; and We make the communications clear for a people who know.
[9.12] And if they break their oaths after their agreement and (openly) revile your religion, then fight the leaders of unbelief-- surely their oaths are nothing-- so that they may desist.

(Just speaking against Islam!)

(The last surah is the small 110th)