I'm not much on the NFL, but the ongoing non-sense with Deflategate and such bears watching. The main reason is that the NFL is grappling with the dual tension of record profits and decreasing public confidence in the leadership of the league.
The biggest thing protecting college athletics, particularly the cash cow that is college football, is the autonomy of the conferences. Will that become the reason the NCAA, with their ongoing publicity and discipline investigation failures, ceases to exists?
If you don't think it'll happen because of the money involved, remember, the NFL is the most profitable sports league in the world. More so than English Premier League (note the caveat at the bottom of the article about TV money), which monetizes everything.
The bigger issue the NFL faces will the money still matter if the casual fan decides the NFL isn't worth their time. The league is owned/controlled by the NFL owners. They control Goodell. Yes, there are issues internally, with some owners supporting Goodell just because he is not no longer in the Kraft pocket (for a great treatment of this, read the ESPN OTL piece), but 'protecting the shield' also means something different to the very savvy business people that own the teams.
As Will Leitch put it: "People love football. But they hate the NFL." I don't buy that all people hate the NFL, but there is a substantial minority of football fans that are starting to treat pro football they way they treated MLB after the strike in 1994. They just stop caring.
Now, the big question is will college football take a lesson from this and figure out a way to not let the NCAA screw up the brand of College Football? Because if they do, the money we see now is the top. But again, the future doesn't seem to matter too much as long as the money comes in now.