Racial profiling, the way I've seen most people argue against it, isn't actually a bad thing.
Here's an example:
A man robs a house. He's described as a black man, mid-20's, driving a certain make and model of car.
In the same area, the police see a black man, mid-20's, driving the same make and model of car. It's not the robber, but the cops can't ignore him because he actually does fit the description provided. But somehow this is racial profiling because they stopped a black man. As if the cops would have a reason to pull over a white, or asian, or hispanic man, or a woman, even though that wasn't the description given.
Funny thing is, had the description been a white man, mid-20's, driving a certain make and model of car, no argument of profiling would be made for pulling over an innocent white guy in the same model car. But if they're a minority, that's sometimes the first thing claimed.
Now, in the Muslims case, randomly searching all Muslims because the current terrorist threat is from Muslims, is wrong. It's not the same thing as looking for a Muslim man for a specific crime in an area like the example above. This is randomly searching a person only because they are Muslim. The police had no reason to suspect the person of anything than being of a certain religion/race.