I would imagine there is a bit of risk mitigation with AF1 as it relates to taxiing on the ground. As you state (correctly I surmise) the best place for AF1 to be is in the air. The worst, is unprotected on the ground. The secret service is great, but I don't see them clearing a mile of taxiway in multiple directions for the safety of the aircraft.
Best to land long, turn off at taxiway and be at your destination with proper equipment nearby as soon as possible.