I'd bet there are tens or hundreds of thousands of foot fungus infections, as well as other infections, that can be blamed on the shoes-off policy.
Or we could blame it on the passengers' lack of foresight. A clear plastic disposal baggie can be slipped over the foot to create a sanitary barrier, and probably costs less than a nickel.
I went through a checkpoint in my lil sock feet 4-5 days a week (sometimes multiple times in a day) for more than a year with no ill effects. Have never had a passenger tell me they contracted any sort of ailment from our floors.
The human body is remarkably resistant to disease!
Also, keep in mind that if you wear your shoes in your house, you're transporting microscopic particles of anything you stepped in outdoors -- including bacteria, germs and most likely bird or animal feces -- to your floors and carpeting.
I'll bet most people who complain about TSA's "shoes-off" rule don't think twice about wearing their shoes in the house and then walking barefoot on the same contaminated carpets!