I have such thoughts as well Banquo, at least since some guys wanted to blow up a train that goes through Cologne and I am now using that route about every two weeks. But then I also wonder whether other people might think I could have a bomb in my really big coffer.
No, I'm white, very white, but still.
I think it's just that they look different, I'm not really worried but they get a bit of extra attention at times, even without reading a holy book. Sometimes it's enough if they're female.

In the end though, I treat them like everybody else, my thoughts or feelings about someone are subject to rational testing before they dictate my actions and I have to say I've had a lot worse thoughts which I acted on than "he might be a suicide bomber".