Nicholas49, I'm open to correction, but I believe the president is commander in chief of the US armed forces in his role of head of state. He is also head of government and in this respect of course, he's different from most governments (with the exception of France), where these roles are usually divided.
So, while as head of state, he is commander in chief, the CO of Air Force 1 is, like the captain, legally responsible and would have the right to divert if need be.
I guess, in the event of ditching, things are easier for the president; everyone else has to swim; he can just walk to the nearest shore.
Seriously, though, I wonder if AF1/2 pilots are taken from the E-4B fleet, or open to other transport fleet pilots - KC10, C17, etc? Even fighter/bomber pilots?