This is one reason why it will be hard to get rid of the silly requirement to take shoes off. DHS has a financial interest in keeping the theater going.
Rules like this that don't really have a point and are applied unevenly (like drug laws, many traffic laws, public intoxication...) are just a lazy way to make sure authorities can make anyone or any group they want "fall in line" while not actually preventing favored individuals or groups from doing what they want. It's the most unfair and unequal kind of regulation, and in general people cant6get enough of it, precisely because they know it will be used mostly against groups they don't like, but they dont have to explicitly identify those groups or otherwise acknowledge their prejudice.