I doubt someone like Troy Smith would take a $500 job. It'd be mini-NFL deals as far as endorsements I think, for someone of that stature.
That's precisely my point. How are athletic departments going to account for, let alone regulate, hundreds of thousands of dollars in endorsement deals being doled out to their players? Not to mention the issues with student-athletes' privacy. Who's to say that a few years after college endorsements become legal, a group of starters for some SEC school sue their University to remove whatever feeble regulation the NCAA builds in to keep an eye on the proceedings?
The amateur status of the NCAA would be compromised as well, forfeiting their tax-exempt status. Not to mention that athletic departments would have to pay for many more people at desks keeping records of all these endorsement deals, trying to keep them straight, all while many ADs around the country hemorrhage money on a regular basis. The current system may seem arbitrary and unfair, but it is the only way to maintain amateur intercollegiate athletics as we know it.
Your comparisons to some of the great technological innovators is interesting, but remember that Gates and Zuckerberg both dropped out of college before making their millions. Zuckerberg was actually in very hot water with the administration at Stanford before he left. These entrepreneurs didn't need an endorsement or benefit system because that's not how the market operates. There is a whole industry dedicated to funding tech entrepreneurs that supports people like Zuckerberg and Gates. It is true that the industry grew up around the pioneering innovators, but the market provided the tools for these people to succeed, and by and large, that system functions as well.