About 57% of football teams made money last year. To quote directly "Sixty-eight FBS schools reported turning a profit on football, with a median value of $8.8 million. The 52 FBS schools that lost money on football reported median losses of $2.7 million." Additionally given that only 14 athletic departments made money, there is very little actual profit coming from either men's basketball or the football teams.
http://sports.espn.go.com/ncf/news/story?id=5490686That doesn't account for the creative accounting practices that are used to pull money from the general school revenues. When I was at the University of Colorado a few years ago there was a large student fee for new training facilities for the football team which was separate from the fee for other sports.
http://www.oregonlive.com/collegefootball/index.ssf/2009/10/new_ncaa_definitions_of_revenu.htmlAlso on the facilities front, the NCAA doesn't count the costs of building facilities as part of the athletic department budgets, nor does it account for upkeep or utilities.
http://www.collegecharlie.com/sportscosts.htmlNor does it account for the fact that monies donated to the athletic departments by boosters are tax deductible so they are subsidized by the taxpayers. Additionally there is no way to know what level of those donations would still be made to the universities without the athletic department.
This link also notes the fact that as a result of moving up to a new conference Cincinnati is having to increase student fees, tuition and give more from the general fund to cover the deficit.
http://www.usatoday.com/sports/college/2010-01-13-ncaa-athletics-subsidies_N.htmGiven that every other department on campuses are being pared down, there's no reason that athletics should be any different, especially when you consider that the department's resources are used by far fewer students, so each dollar per student is higher. Also the student athletes in the two big men's sports are generally of a lower academic level than the general student body (with some schools being notable exceptions like Stanford), this additionally detracts from a school's central mission of quality education.