I've had 2 "genital pat-downs" when going through airport security. Not really a big deal. You unbutton your pants, pull them down a bit, with underwear still on, and then a guard with gloves on "pats" the genital area.
Whatever the reason is that I was pulled out of the line for the "genital pat-down", I don't know. A little embarrassed at first, but quickly go over it. More embarrassing was "beeping" when I went through security, had to empty my pockets, and had a Magnum in it's foil packaging in my pocket, which was making the alarm go off.
mako- that was San Fransisco, right? I think you've been had. If you were pissed off about it, I'd submit a letter of complaint to the TSA website.
..Got taken into a private room by a guard in amsterdam (IIRC) a few years ago. Had to drop my trousers and he had a feel around my junk and then just said "hmm, must just be your big package" (I'm not usually that big soft - must have been a good day). Nice ego boost - have considered wearing a metal cock ring when flying since to improve the chances of a repeat performance hehe.
Funny experience at a California airport recently: As I was about to enter the full body scanner, the female TSA agent asked me if I had removed all items from my pockets. I patted my pockets and found my boarding pass in a back pocket, which I handed to her. She said "You have something in that pocket", pointing to my left front pocket. I dress left; it was my bulge. Just to show her nothing was IN the pocket, I put may hand inside, came up empty and said "No, it's just me."
She looked flustered and would not look me in the eye after that.