The House Speaker is required to fly on military aircraft rather than commercial carriers, as are other high ranking political officials. I don't recall now if they enacted a law or it's just House rules, but the change was made for security reasons in the aftermath of 9/11.
The flap over Pelosi when she became Speaker was that she requested a bigger jet than Dennis Hastert had been using. The Hastert's smaller jet that carried him home to Illinois didn't have the range to get to San Francisco nonstop, so to this conservative it was a reasonable request. However, I think the issue then got heated up because Pelosi wanted something bigger than smaller planes that could make the nonstop run.
I would bet dollars to donuts that Boehner reverts back to a Hastert type plane for his short flights to Ohio.