Have you ever had your time onboard a plane extended because your flight is circling an airport, waiting for a terminal to become clear so it can land? It's enormously annoying when that happens - and it's an annoyance the President doesn't have to deal with.
Air Force One has primary clearance wherever it goes. That means it can just land on the tarmac without approaching a terminal. It also means anything else in the air has to wait until the President has disembarked before they can approach!