Haz,
I too understand the hostility that is sometimes directed towards Muslims but the fact is that not all Muslims (in fact, very few) agree with terrorist tactics.
The Muslims of Arabia only actually constitute only 20% of the world population, and even there only a small margin supports such terrorism. The fact is, most Americans still know very little about Muslims. It's better than it once was, but even now people don't know the differences between Sunni and Shi'a. They know nothing about Sufi mysticism or Druze secrecy or the Yazidis or Muslims in India who blend Hinduism with Islam.
In fact, most Americans don't even know the five pillars of the Islamic faith. Most don't even know the true meaning of Jihad (it's "struggle" and is only expressed in terms of "holy war" in very rare cases). There are so many cultural differences and sects that we just tend to lump them all together. We are altogether terrified of the unknown. In fact, most Americans would be dumbfounded to know that a Protestant Christian created what we know as the Modern Arabic Language. Or that the founder of the Popular Front for the Liberation of Palestine was in fact, an Orthodox Christian. In fact, Americans believe that the Taliban in Afghanistan represent mainstream Islam (they most certainly don't and they get away with it because the literacy rate is 11% and the people can't even read the Qur'an in the first place).
I'm a flag-wavin', gun-toting, bible-thumpin' Christian, but I'm also a student of Middle Eastern studies and the fact of the matter is that we are largely ignorant of what happens in the rest of the world.
There is a good documentary available on Youtube that goes over the perceptions of Arabs in MSM and film. It's called "Reel Bad Arabs" and it's a good one to watch:
http://www.youtube.com/watch?v=ewaox9UA6NE