One thing that complicates this is Title IX. If you pay football players directly, suddenly you have to pay an equal number of female athletes. Now you have women's softball and women's soccer players getting paid. And not only that, but if I pay Star QB $10m per year, I've got to pay the female players $10m per year. So some female sports teams will be uncompetitive with others, and those teams will need their own division.
Ultimately you end up with some teams in the NCAA not paying players and some in a completely separate non-NCAA professional league for all sports and the two groups never play.