I think schools like Stanford recruit players who were also good academically in high school. I mean look how little players they signed during signing day - or at least the ones that were considered top recruits. I believe that when high school players visit campuses, Stanford probably has a high academic standard as a student athlete that most of them are probably turned off by it and would rather just focus on football. Andrew Luck, for example had a major in architectural design and he even decided to stay his senior year.
It is a sad reality of college sports, but my guess is that the portion of student athletes who don't graduate probably just wanted to get the hurdle of college before going professional over with. Just like the NBA where students have to attend just one year of college before they can jump (not sure if that's been increased though). It was an improvement where just can just jump from high school to pro, but I think they should at least be juniors before they can move on to a professional team.