One thing seems to have been overlooked by those contributing to this thread. I fly for an Arab airline, and regularly fly freighters in and out of JFK. Even though we go through the Cargo side, we have the full security aggro. The pilots on the passenger flights get the full treatment as well at the passenger terminal.
We don't get treated any differently, it seems, than the other contributors to this topic have been, but I do realise that the US government is absolutely paranoid about Al Qaeda sympathisers working as pilots within airlines (especially ours!). This is extremely unlikely, but they feel that they have to give the idea some credence.
So, for the sake of political correctness, and to avoid the dreaded "profiling" they treat all pilots the same, irrespective of airline or nationality. To do otherwise would provoke serious diplomatic reactions.
So, I think we need to remember that American paranoia in respect of possible infiltration of our profession is the root cause of this. Of course, an Al Qaeda pilot could do his stuff and still be clean at a security check!
Out of JFK, they won't even let our company take off on 31L! That points towards downtown Manhatten, so we are forced to takeoff on 22R, or 04L, what we laughingly refer to as an "Al Qaeda Departure, Bin Ladin Climb"!