There are some peaceful, tolerant verses in the Qur'an. But the violent, intolerant ones have nullified them. The Qur'an itself explains what to do with conflicting verses. If two passages conflict, it says, the one written later is better than the one written earlier. This is called the principle of abrogation.
The bad news for non-Muslims is that almost all the peaceful passages were written earlier, and the violent ones were written later.
The entire Qur'an was written by one man over a period of 23 years, and his revelations changed over that time. They became less tolerant and more vengeful.So that explains part of the confusion: Peaceful and tolerant verses are accurately quoted, and so are the intolerant and jihad-oriented verses. But there's more to clarify here.
RTWT. If you haven't grasped the concept of taqiyyah by now, you'd better learn it quick.