I can see how it might look like a bomb to anybody who knows little about the insides of a clock or electronics in general (or bombs, I guess).
But to go from taking precaution and figuring out what the hell it is that he had to "you're under arrest because we think you're 9/11" is ridiculous. Just an abundance of stupidity, with probably some fear and hatred sprinkled in. But mostly stupidity.
While I agree about the stupid factor being a key thing, I also think the fear-and-hatred quotient is much higher than you seem to... unless you think they would have treated a blond kid with a WASP-y name the same way...