Student athletes' biggest protection from retaliation is probably their incredible power over the institution and high level of visibility, as demonstrated by the actions of the Mizzou players during #concernedstudent1950.

Football players, at least in D1, have also been determined to at least have some of the rights to concerted action protected under the NLRA:

https://www.insidehighered.com/news/2017/02/02/nlrb-general-...

Of course, while that does protect them from their current employer (the school), I don't think it can protect them against the reluctance of a potential future employer (like the NFL).