This is a very difficult and intertwined issue. It can't be denied that Islam is a religion of violence and aggression, Dan knows more about this than I do because I haven't researched Islam in as much detail as he has. But one does not have to look far to see the effects of Islam. Do we see any area in the world where there is as much conflict as the Middle East? No - this can be explained by the location of the Middle East, that is true, but to a large extent it is due to the explosive, violent nature of the people who live there. There are also other issues such as the oppression and lack of education of women, are there any other countries in the world as rich as Saudi Arabia and the UAE where the level of education of women is so alarmingly low?
It doesn't stop there, in light of the recent protests, have you ever seen any other religious group that is so overtly violent? I have never seen Jewish, Christians or any other religion react in such a way. It's also appalling the way children are brainwashed into believing that "jihad" and the protection of their religion should be placed above all else.
On top of that, there is a reason why the world makes associations between Islam and terrorism, where there is smoke, there must be a fire, these things don't come out of nowhere, it is because of the aggressive nature of Islamic theocracies.
Either way, of course, you are right, there are moderate Muslims who are harmed by the negative view many have of the Islamic religion, but considering so many of the issues which surround Islam around the world, I am not surprised this is the case.