Same thing happened on my flight from Baltimore to Tampa today. When I checked in, the agent put a big mark on my boarding pass and told me that I had been randomly selected for a secondary security check. At the gate, I was taken to a separate area and my bag was hand searched (everything removed and put back in), I got the wand, and I was patted down. There were about a dozen others, all were of Middle eastern background--Muslim, Hindu, etc. I agree with the notion that it is a way around racial profiling...I guess I was the token white.
This was my first experience of this in all my travels since the attacks. I ponder if it is related to the "increased threat" the FBI announced yesterday.