Related to my point about people judging the Bible on a different set of standards than the Koran, here's Conor Friedersdorf writing about the backlash Muslims have faced since 9/11.
It sounds to me like there was a significant backlash in 2001, and that even after that, hate crimes against Muslims stayed from three to five times more likely than they were before the terrorist attacks. And, of course, hate-crime statistics are hardly the only valid measure of discrimination.
We need to stop blaming all Muslims for the actions of a very select few. We don't tolerate that with any other religion or ethnic group; we shouldn't tolerate it against Muslims, either.