I don't remember very many times they would send a crew commercial (unless we were picking up a plane out of depot or something). You would have a bunch of gear, pubs, etc. to bring along, and with an airplane like the E-4, the crew probably carries classified materials that you wouldn't want to stuff in the overhead...also, they do need to fly a certain number of sorties to maintain proficiency, so it serves as a training mission as well as repositioning flight.
I guess they could send them as pax on another flight, but unless you happened to have a cargo/pax flight heading between the right places, you end up tasking another aircraft/crew for the trip, and probably don't save very much if anything that way.
[Edited 2010-01-07 19:30:10 by moose135]
KC-135 - Passing gas and taking names!