Some Muslims, for example, Ismailis and Ahmadiyya Muslims, believe very strongly in tolerance - and they are themselves the subjects of persecution in many Islamic nations, because they're not recognized as "real" Muslims.
How much of a link is there between what the ordinary Sunni or Shi'ite Muslim believes and terrorism? It would be nice to be able to say that there is none, because all religions teach peace and non-violence.
In practice, though, different religions do teach different things. Even though Jesus told his followers to "turn the other cheek", except for a few denominations like the Quakers, the Mennonites, or the Jehovah's Witnesses, Christians are by and large not pacifists. Pacifism - and vegetarianism - are part of Buddhism, and even if not all Buddhist nations have a perfect record of pacifism, the religion has had a significant impact in that direction.
It is a fact that Shari'a, sometimes known as "Islamic Law", puts non-Muslims in a position somewhat similar to that experienced by black Americans under segregation in some respects. Thus, members of a non-Muslim minority in a Muslim nation, such as Coptic Christians in Egypt, often do not have recourse if they are wronged by a member of the Muslim community.
Islam prohibits rape, but Islamic Law sets up a situation where someone perceived as a Muslim has a good chance of commiting that crime against a member of a minority community with impunity.
As far as I'm concerned, an entirely appropriate response to that is to partition the country where this is happening, so that the members of the minority community now have an international boundary behind which they can be safe, and the ability to defend themselves. That is what happened to Palestine originally. And the reaction of the Muslim nations around the new country of Israel was to descend on it to drive it into the sea.
The idea of unbelievers asserting their own human rights, taking over dominion of the land they live on, rather than living as submissive subjects of Muslim rulers, was viewed as an outrage against the natural order of things.
That's not necessarily some sort of Muslim disease, though. Somehow, I think the United States would have taken it badly if in, say, 1920, the black people of America decided they had had enough and decided to partition your country.
In being capable of bigotry and injustice, Muslims aren't all that much worse than anyone else. Their real problem is, particularly after 9/11, that because they believe firmly that an all-powerful God is on their side, they don't realize that unlike the United States - that was highly unlikely to have been invaded by Britain over its treatment of its black minority - they're not really in a position to get away with that kind of thing any more.
When a Muslim country mistreats a non-Muslim minority, to outsiders that looks like proof that the Muslims of that country, at least, don't really think of non-Muslims as real human beings. So if they're not terrorists, it's probably only because they're not brave enough - not because they think it's wrong.
The Western world's progress towards equal rights for religious and racial minorities was slow and painful. And now terrorism has put the Islamic world under such an intense spotlight that it may have less than a decade to move from the Middle Ages to the 20th Century to avoid disaster. It isn't fair.
But that doesn't stop it from being real.