If they want to, sure. But first of all, they don't, they distribute about half a billion dollars to the universities that want to be under the NCAA's umbrella. SecondIy, I imagine if the NCAA wanted to keep all the revenue for themselves, universities would find another governing organization to conduct championships and set guidelines for their athletic programs and conduct championships.
The NCAA makes the rules, period. Athletes can either choose to follow them or not. It's capitalism. Those athletes that think they are getting exploited can go make as much money as they want to any way they can, they just can't compete in NCAA sanctioned events. There was nothing stopping Johnny Manziel from signing as many autographs as he wanted to for as much as he could get, he just couldn't play college football anymore had he chose to exercise that right. And if he doesn't want the school to make any money off selling #2 jerseys, fine, sue the NCAA I guess. The school will stop selling #2 Manziel jerseys and Johnny Football's college career will be over. Maybe everyone will be happy then.