I, as somebody who travels a lot, don't think it is much worse than an hour and a half flight. So long as your travel does not cost you a good night's sleep and you get nonstop flights where possible, the extra couple hours in the air is de minimus.
Now if you're Texas Tech, for example, and you have connections to get from Lubbock to Provo in Thursday with a game at UCF the following Saturday or Sunday, then travel wear and tear would be a handicap.
My guess is the B12 tries to minimize that type of travel schedule.