It is a well-known fact that AQ's goal is the return of the Caliphate. To do this, bin Laden needs the secular regimes in the MidEast overthrown and replaced with Islamic theocracies of some sort. In order to have this accomplished, he must generate his own army, and since he's not a nation-state, must rely on a popular groundswell. Given the violent history of the region and its people, and the fact that bin Laden and Co. believe they took down the Soviet Union by bogging them down in Afghanistan, and their goal doesn't seem so impossible. (I agree with George Friedman's thesis that generating this conflict was AQ's aim with 9/11 and that so far bin Laden has gotten exactly what he wanted.)
It's just plain common sense not to inflame millions of people who are integrated into various societies. Going after violent criminals is an obvious and legitimate response to things like the death of Van Gogh. Bombing and burning down Muslim schools is obviously not directed at this murderer (we assume nobody thinks a bunch of six-year-olds did this) but at the Muslim community in general. The fact that the ethnic climate is eliciting state-sanctioned racism is alarming. Worse, however, is that all of this might just give AQ exactly what they want.