But, the less obvious reasons surely include maintaining the function of the huge TSA security apparatus put in place after 9/11. The stated function of the TSA is to protect passengers from attack. The unstated (and unacknowledged function) that has perpetuated the practice despite every traveler hating it (and its obvious futility), is to intimidate travelers and provide a convenient mechanism of crowd-control. Step out of line (literally) and you will be treated as a potential criminal. There needn't be an official policy to do so, the benefits of the system ensure its continuance via other (stated) motives, not least the profit motive of the supporting economic interests. The upshot is that travelling via plane in the past 20 years is one of the many small lessons for living in the security/surveillance state. You must obey. Moreover, we see the logic of the security/surveillance state incorporating this convenient control mechanism by now restricting (or implicitly threatening to restrict, which is even better) the travel of domestic antagonists of power. If we had discontinued taking off our shoes, the symbolic effect of dispiriting and weakening the public (literally making us vulnerable in our unshod feet) would be unavailable now. Why would the administration willingly relinquish such a useful tool for managing the population? Of course it wouldn't. It would we more amazing if it had.
Now, we will likely add further controls on travel in the form of digital health passports with infinitely more possibility for government mischief. When/if the pandemic ends, do you believe the passports will be discontinued?