That's absurd. I'd be willing to wager big school football makes orders of magnitude more than minor league baseball, hence the coaches do as well.
The biggest problem was that the best players in the world weren't playing in the XFL. Div I-A college football doesn't have that problem. The lower divisions do, though. I doubt many Div I-AA or Div II coaches are making $1MM.
College football programs rake in huge money, and therefore the people responsible for their success do too, whereas minor league baseball teams do not, and therefore their coaches don't.