For smaller hops and smaller airports that may not be able to take on a fully-loaded 747, the Air Force has a whole fleet of other aircraft that can handle any need the President might have. And after all...ANY Air Force aircraft the President is on, whether it be a 747 or a Piper Cub, automatically has the callsign of ‘Air Force One’.
There’s the security contingency that travels to his rallies, too. NOT a small operation.