I get pulled out of the line for additional security checks nearly every time I fly. Even when I didn't set off the metal detector, I have often been asked to step out of the line to be wanded. One male TSA agent started to wand me before getting a better look at me, and called out, "Need a wand check for a female over here!" Another male TSA never noticed, or didn't bother to get a female TSA agent.
Even with the backscatter scans, I get pulled out and patted down. I've never felt inappropriately touched or treated less than professionally. But the frequency of searches does suggest that it's not entirely random. My ex-gf and I traveled together a lot, and since she never got pulled, it was all the more obvious that it was specific to me. It made her angry that the TSA is targeting butches as if we're terrorists, but it kind of amuses me. I'll admit here that I'm usually the last to notice homophobia directed at me, and when I do, I see it as their problem, not mine.
Oh, and I've had my palms swiped with a piece of paper that was fed into a machine that checks for trace explosives. On three different trips.
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The irony here is that I'm a U.S. federal employee (Health and Human Services, not Homeland Security). I've been thoroughly documented and verified by dozens of government checks as a routine part of my job, and use radio-chip card keys and biometric readers (fingerprint scans) just to access my office. I'm used to government scrutiny and as long as it's done professionally, I take it in stride.