So while Idaho St. likes its 500K payout to play BYU or Utah and they would probably play 2 of those games a year, their entire model is not 100% dependent on those games.
As long as they are not losing a ton of money, then many schools are fine with paying out reasonable amounts to the Athletic departments. They are just another part of the school's expenditures, like the math department or the language department.
Idaho St's football coach is not making a huge salary.