Well, when you give pilots the unilateral power to remove someone from a flight and there are 75,000 flights every day there are bound to be some abuses. Not sure this is surprisingly or that it necessarily even indicates that the system isn't working.
The pilot is responsible for the safety of everyone on board.
The question is, was the behavior of the passengers a credible threat? My guess is that the TSA & the airline (the pilots employer) have told him to put anyone off if there is even a hint of noncompliance.
One of my favorite "hidden" quotes from the movie Brazil may be applicable: "Suspicion Breeds Confidence"
