If we look at the chronological Quran, it is clear that it seems to advocate peace and tolerance only before Mohammad's flight to Medina, and after, they turned inherently violent. Why?
Quran (2:216) - "Fighting is prescribed for you, and ye dislike it. But it is possible that ye dislike a thing which is good for you, and that ye love a thing which is bad for you. But Allah knoweth, and ye know not."
Quran (4:74) - "Let those fight in the way of Allah who sell the life of this world for the other. Whoso fighteth in the way of Allah, be he slain or be he victorious, on him We shall bestow a vast reward."
Quran (8:12) - "(Remember) when your Lord inspired the angels... "I will cast terror into the hearts of those who disbelieve. Therefore strike off their heads and strike off every fingertip of them"
Quran (8:39) - "And fight with them until there is no more fitna and religion is all for Allah"
Quran (9:5) - "So when the sacred months have passed away, then slay the idolaters wherever you find them, and take them captive 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."