Other TSOs have answered this before. The short answer: force of habit.

The long answer: TSA critics, here and elsewhere, often complain that screening procedures are wildly inconsistent between airports --- or often, between screeners at the same airport. TSA does strive for some level of consistency. It teaches its screeners, when performing a patdown, to perform the same actions, in the same sequence, every time. Ideally, this should lead to a more consistent experience.

Of course, since many passengers choose to wear socks, or are unable to remove their footwear for medical reasons, the standard patdown includes a patdown or wand-scan of the foot area.

Now, here comes a passenger with bare feet (for example, one wearing sandals without socks). Clearly, a patdown or wand scan of the bare feet is not necessary per se. But between force of habit, and the training the TSO received to conduct every patdown the exact same way, it's entirely possible that the TSO will end up patting down or wanding the bare feet.

There is a bit of a contradiction at play here. Many TSA critics (including myself) want TSA to standardize screening procedures across checkpoints, so that everyone knows what to expect from screening every time. On the other hand, many of those same critics (again, including myself) want TSA to deviate from those procedures when it clearly makes sense to do so. It's a little hard to say "always follow the rules, except when we don't want you to."