I've never been able to figure out the Secret Service decision process for deciding which airport the President lands at.
Minimizing the ground transport distance seems to be a priority, but the ability to secure the aircraft parking area also seems high on the priority list.
Both airports would be fine as far as the runway capacity.
Some times it appears that they do not like USAF
or other military bases which have a moderate level of flight activity. I have no idea how busy Offutt is these days. The Secret Service also seems to not like USAF
bases with strategic aircraft like bombers.
I think that might have to do with difficulty getting civilians like local officials, media and such cleared to get on the base for AF1 arrival and departure events.
[Edited 2012-08-09 18:15:49]