University protests are probably as old as universities themselves, so I don't have an issue with student protests in general which disrupt the functions of a university. It happens. I don't think it's the best avenue for the student-athletes involved to voice their concerns, if only because it affects their teammates. Provided they have their teammates' backing, then I don't have a big issue with it.
Even if the university would have a right to pull the student-athletes' financial aid, they'd be idiots to do so - again, they'd get killed on the perception front.
I think it's misguided to blame things on the Obama administration. Sports-related protests are nothing new. It has little to do with the administration currently in charge.