Football for the vast majority of schools is just a loss leader.
That's true if you're looking at FBS and FCS combined, but if you look at FBS only, not so much. That's why there's still great interest in upgrading, and the seemingly endless proliferation of bowl games.
Several years ago, I did a study on what revenues and profits are made by all 120 (at the time) FBS programs. Keep in mind that the numbers this anaylisis was based on were six years old at the time, so by now these are 12-13 year old numbers. They broke down like this:
The top 20 teams made huge profits from football, anywhere from several million up to 50+ million for the year.
From 20-50 or so, teams all made profits, but anywhere from slightly to considerably less than 1-20.
From 50-80, they either made a tiny profit, 1 million or less, or they about broke even, but none lost money. As an example, a bad FBS program like Vanderbilt was at 51 or 52, but still made a profit of a little over 1 million that year.
From 80-120 were the money losers, some very modest in the $100-$300k range, some into the small millions and a few several million or more.
Those numbers have likely skyrocketed at some of the top 20 behemoths since then. Several years ago Texas reported an 83 million profit from athletics, and likely 90 percent or more of that was from football. That's close to 75 million, likely about 50 percent more than 6-7 years prior at 50 million.
This is why the most successful FCS programs are generally interested in jumping to the FBS level.
It's true that the bottom 40 teams of FBS and the FCS schools have to view football as a loss leader, but making it to the FBS top 50 is the goal. They make money, and about the top 25 make tons of it.