I find it strange that some Muslims still wonder why they are discriminated against or feared by americans. Isn't the answer obvious? 
Yes, not all Muslims are terrorists. But all the terrorist do seem to be Muslim.
How is one to know the difference? You can't, that's the problem, and its a much bigger problem than Muslims will admit. Of the billion plus Muslims in the world, perhaps several hundred million are radicalized and either hope for America's fall or actively working to make it happen. It's no small threat, fears are not unfounded.