Perhaps it was a 'Jihad Joe'.
But seriously, the agenda of the security screeners at US airports is seriously flawed. For example, every time I have been through the security checkpoint at Boston Logan, I have been selected for a special search despite being in uniform, while passengers, some of them of middle eastern appearance just walk through. And it's not just Logan (one of the biggest cock-ups of an airport I have ever come across IMHO). I generally notice that flight crew are selected (despite not looking too shifty) more regularly than the pasengers are.
I can appreciate that security should apply to everyone, but don't these muppets realise that flight crew are already on the flight deck and won't need weapons to force their way into the cockpit? Or perhaps they believe one pilot may try to disable the other and do something - as in a Tom Clancy novel. Better not let them know there's a fire axe in the cockpit.
Security effort would be better spent concentrating on the passengers and not checking the crew out of petty jealousy or whatever other motive that drives these individual's undeveloped cognotive process.