Actually, over 90% of NCAA Division I football programs lose money*. And in many situations, even those that "make" money are actually making money only for the athletic department (staff, facilities, etc.). The reality is that these teams are heavily subsidized by state money and student athletic fees.

I think this is fine sometimes, but we should apply a matrix measuring the cost of various sports as compared to the non-financial benefits. Hockey, for example, is very expensive due to the number of players involved, equipment, ice time, etc. Attendance is low because UAA hasn't really had a competitive hockey team in 20 years or so; I doubt they'll ever compete again. In contrast, volleyball and basketball cost very little, primarily because they have fewer players, minimal equipment needs, and play on a normal gym surface.  They also have very good attendance because the programs are successful.  

*http://www.ethosreview.org/intellectual-spaces/is-college-football-profitab