Earlier quoted context omitted.
Destroying the aircraft in mid air isn't really the threat any more, though. The threat is using the airplane and its occupants as unwilling kamikaze weapons as in 9/11, and with the armored doors on the flight deck now it's unlikely the aircrew will allow the aircraft to be hijacked no matter what you bring on board. There's a reason the flight attendants stand in front of the door when the pilots have to use the wa…
Shoes are obstensibly removed to prevent the destruction of planes, not their hijacking. The problem of planes being hijacked was solved around 10am on 2001/9/11, before the government got involved. And if passengers fighting back isn't enough, locked cabin doors should be. Incidentally, passengers kicked the shit out of the would-be shoe bomber too.
Perhaps that's the stated reason, but I think you and I both know it's security theatre, just like the "no phones in flight" rule.