Usually the Secret Service chooses the closest civilian International airport to the destination in order to have the shortest/most secure route available for the motorcade upon arrival.
There are also concerns with civilian accommodations - as the President often travels with a large group of the media and some VIPs, the choice of using a civilian airport instead of an air base for these trips allows the USAF to maintain base security.
Press coverage and welcoming ceremonies with local dignitaries are also more accessible when it occurs at a civilian facility.
Don't know about aircraft ops, but I can tell you that the number one priority of the PIC is the safety of the airplane and it's occupants - not unlike some other PICs around here, I would think.
