Where does the money earned by universities in the USA from sports activities go?
Revised answer:  At my university, where football is big, the athletics department supports itself, and that some of the money goes back to the university, but the only specific instances I know of are donations to the art museum and history of science collection.
That said, I am sure most of revenue generated stays within athletics.  

For instance, this article talks about the most profitable football programs, and out of Alabama's $110 million revenue in 2013, $6.5 million (5.9%) went back to "academic programming."  However, the details of how that money got used, and how much actually went back athletics (via athletic scholarships) is unclear.  In any case, this is a small amount of the university operating budget.  Florida that year gave the most back to academic programming $7.2 million, but the general and educational expenses were $524 million.

However, most universities lose money on athletics (see, e.g., this and this).  These universities make up for this by doing things like charging students fees for the athletics program and cutting funds to other programs/units.  Even some of the ones which are termed profitable get large subsidies (e.g., student fees)--only 7/230 Division I athletics programs did not take subsidies last year .  These articles say that even the donations athletics help generate goes back to athletics and that a relatively small amount of the athletics costs (about 16%) goes to student aid.