The Air Force One plane is one of the heaviest guarded planes with a very large convoy of soldiers, extensive array of weapons and detection systems, and air support system. Yet, the bad guys had no difficulties in disarming a "small" group of soldiers and entering the "empty" plane guarded by a few soldiers.
When the president of the United States is travelling to the remote locations, it is usually done with a group of Marine One helicopters rather than long drive with the motorcade. If the president is threatened, the option is to evacuate him or her to the Air Force One (or US embassy if necessary) as quickly as possible and lock down the airport quickly. Yet, the president wasn't anywhere near or inside the Air Force One when the threat was detected.