Royalty
There are probably costs to Bohnner flying domestic flights that are not being considered. Additional secret service security being an obvious one. Is he unnecessarily putting himself at risk of attack? Problems involved with other passengers being delayed or inconvenienced is also a consideration. And I seriously doubt he is flying in coach. First class ain't cheap either. He may be picking up his own tab but I doubt all his security is.
For your average Congressperson domestic flights may be fine, but for the SOTH, who is a very high profile leader of our government, I don't begrudge Air Force transport. I'm sure many military leaders also use them.