Where did I say they should get paid?
I said that using things like names and likenesses should be allowed without the players having to be treated as professional athletes. The argument that you can't make money off the players is silly given how much money is being made in revenues from things such as broadcast rights, season ticket sales, etc. That money wouldn't be made if it weren't for the players. Athletes should be able to maintain amateur status and have their name appear in a video game.
I would think most football programs invest their money into their coaching staff and facilities rather than investing it back into the university. Universities tend to have endowments separate from their athletics budget. Rice, for example, has endowments from historical investments as well as donations from alumni. As an alumnus, I can categorically choose to donate to something, such as the football program. I think it was TCU that a few years ago had a few wealthy alums donate to the football program which resulted in a sudden splurge in facilities expenditure, which (not coincidentally) lead to their team getting really good.
It may be different at UT, which has by far the highest revenues of any other school, but I think in most cases the university budget contributes to the athletics budget, which in turn contributes to the football budget, not the other way around.