As I see it and understand it, the ncaa was to keep schools from organizing outside of conferences... i.e. UM or Auburn since we're aiming at them, get slapped hard by their conferences in this fictitious example, and decide "whatever, we'll just leave the conference!"... which would trigger the conferences appealing to the ncaa to sanction any schools from scheduling the offending schools without full membership into that conference- which requires agreeing to things...
It closes an escape hatch, in other words. The ncaa wouldn't have control over the school, per say, but they'd have some control on who that school plays- if any- by leveling sanctions against them.
They just grew beyond their purpose and kinda killed themselves. The conferences haven't, but they still need some sort of binding contract with other conferences and all of the sport else there would be a lot more independent schools than there are. The ncaa still provides that.