Probably referring to customs / immigration.

OP: I'm active duty and have never had any of the problems you are describing, especially when returning from deployments. I've never seen or heard of anyone calling military out of line and sending them for further screening. I can't imagine any TSA screeners being extra rude to service members, as quite a few are ex-military themselves. Maybe they have dealt with servicemembers coming through their checkpoints with arrogant attitudes and have developed negative stereotypes.