I suspect that bloodymindedness has more than a little to do with this incident (possibly by both parties).
Mere hours before this incident, at JFK, my F/O politely asked if they were going to put some carpet in the screening area since everyone was padding around on the cold floor in their socks, and he received a very hostile reply to the effect that higher ups are in charge of that, move on and shut up.
The poor purser, who was right behind him, was selected for random check.
I refuse to be convinced that any would-be terrorist would announce to security that there was a bomb in his shoe and thereby attract extra attention, so that no matter what bad taste- it would have been obvious that this was an attempt at an ironic joke.
I suspect that the Freedom Fries Factor crept in there too.
No doubt it could have been handled in a less heavy handed way.
Hope it doesn't deteriorate into a childish tit for tat game.