Whether the NCAA is being questioned over it's usage of athletes without providing fair market compensation, their arguments for why they should be considered a not-for-profit, why they shouldn't be considered a monopoly, why they shouldn't be responsible for providing workman's compensation etc. I think that at the end of the day, the NCAA's last defense is that they provide a (free) quality education to student-athletes and this fact gives them a lot of lee-way.
If the NCAA muffs the UNC decision, then this last remaining barrier falls as the whole concept of providing a quality education is revealed as a complete sham. Losing that claim opens the floodgates from many possibles angles of attack. Whether it comes from the courts, from the US Congress, or from other organizations (including a mutiny from within) I don't know. It could come from all angles.
FWIW, here's an analogy. The NCAA is kind of like the old Soviet Union. Sure they look formidable from afar but when you look at the details, you see a whole bunch of states that have been joined together, and largely kept in place through fear. But once there's a vulnerability seen, the dam can break.
In terms of the NCAA, there's a whole lot of schools with diverse interests, resources and goals. It's a constant struggle to keep this coalition of schools together, even with what seems like unassailable power sometimes.