That Bush was better than the craziest Republicans of his time about not stirring up hatred against the domestic Muslim population isn't very surprising -- he was President.
As President, you've got to deal with Muslims abroad, even if it's just to make some of them play along with your ridiculous wars against other Muslims abroad. I imagine that it helps with that if you can not look like an instigator of massive anti-Muslim sentiment within the American political scene.
There's also the possibility that stirring up anti-Muslim sentiment will result in violence from one side or another. While it could play out in such a way that you could politically capitalize on it, that's a dicey proposition.