I have a cheap pair of "shower-shoe" flip flops that I wear through the WTMD. My sucess rate has been very good with only one negative incident that was clearly a power-tripping TSAer. (search for "scoot" and "wtmd" to read about it.)

Many TSAers (and other pax) comment that it is a good idea. I even had one loud TSA screamer/barker who was shouting "all shoes must come off" to the line actually look down at my feet and then say (still in his loud screaming voice) "not you."

I do not put my sock feet on the floor, period. About six months after the shoe carnival started, I got a virus on one of my feet that took over 18 months to go away. I don't frequent a gym, dorms, or other foot-condition prone places, so I'm pretty sure it came from an airport. When I've been stuck without the flip flops (bag lost by US on international travel), I take the secondary, insist on a chair, and refuse to put my sock feet on the floor.