From a screener point of view, our job is to make sure certain shoes are either screened by x-ray or scanned by ETD sampling. It's the passenger's choice. We cannot tell you to take off your shoes; however, we CAN recommend you remove them or undergo secondary screening. Again, it's your choice.
No TSA screener, lead, supervisor, screening manager or FSD can put anyone on any no-fly list or selectee list.
One thing that has always puzzled me is why the airport management doesn't clean the checkpoint more often. The janitors are hired by the city. It would make more sense for them to clean the one area where passengers are more exposed to dirt and bacteria than anywhere else in the airport: the security checkpoint. On top of that, there are often spills, and it takes a while before the maintenance personnel respond to our calls. Just makes sense to have someone essentially assigned to the checkpoint to periodically mop and sweep the floors and to respond immediately to spilled Starbucks cups.
While I'm not disputing that it's possible to transmit bacteria on checkpoint floors, I doubt that it's as easily transmitted as the article tends to suggest. A note to my critics: I advocate keeping the checkpoint clean as I just posted above; however, I don't think that the checkpoint is a public health hazzard. It may be for some, but not for the general public. But for those who want to give in to the panic, consider the following: public phones, public toilets, any seat in a public area, door handles, even the silverware used at public restaurants are subject to the exact same risk of exposure to bacteria. My point here is that you have to draw the line between a reasonable concern for sanitation and an unreasonable paranoia.
But here's the real kicker. You KNOW you may have to REMOVE your shoes when you get to the checkpoint. Why do people still travel sockless? My standing recommendation to travelers has always been to pack either a spare pair of socks or flip-flop shower shoes exclusively for checkpoint screening. Wear them temporarily while screening and, after you've cleared the checkpoint, remove them and any transmitted germs from your feet and either pack them inside your carry-on or (if you're really obsessed over this) throw them away. Either way, a little bit of reasonable prevention on your part certainly sounds smart.