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http://www.ncaapublications.com/productdownloads/REV_EXP_201...

BCS: "Between 50 and 60 percent of football and men's basketball programs have reported net generated revenues (surpluses) for each of the five years reported."

Translation: football makes money, other sports lose money.

FBS: "Only two percent of football programs reported net generated revenues."

Translation: When your program sucks, your revenue sucks too.

Also note that all 14 programs that made money overall were BCS teams.

That may be true but it's not a direct rebuttal to the previous comment.

Does Texas' $3M coach bring in an additional $2.9M+ per year compared to if Texas hired a coach for $100,000?

That doesn't disprove the statement. If may very well be that the football (or whatever) program turns a profit and the rest of the athletic department loses more than the profitable program makes.