Since military bases are, by and large, off-limits to (most) civilians anyway, I can't see the security of the aircraft being a problem as there is security of the station 24/7. At most I'd guess those on guard duty at that particular base are armed. That was certainly the case when I did a brief stint at a Naval dockyard on work experience.
I believe the USAF also carry the Marine helicopters and the crews which transport the President by air. He likes to take them everywhere he goes if possible, and I can't see any reason why it wouldn't be possible in the UK. So his security isn't really an issue since the venue is surrounded by plod and other employed security personnel, and the airspace is off limits to civilian aircraft.