That message, should an average American (not a Thiel fellow) take it to heart, is demonstrably and empirically not in their self interest. Period.
Thiel Fellows are some of the brightest of the bright; of course not attending college won't hurt them in the long run. And accepting a prestigious fellowship will certainly help, at the very least in the short run. So the fellowship makes a lot of sense, and no one claims fellows were hurt just because they return to academia.
However, the fact that 1/2 of recipients of a very prestigious award (and the associated money/opportunity) decided it was in their best interest to return to university is important. It's important because it cast a pretty serious shadow on Thiel's view of college as unnecessary (or over-rated or not in most people's interest... however you want to hedge his claim.)
So while Thiel fellows aren't hurt per se, anyone else listening to the "don't go to college" advice can consider this a rude wake-up call.
So. That's why it matters.
BTW: recently talked with a HS student who got into Harvard (low income, so full ride), but some startup guy was pressuring him to not go to college and instead take a dev job paying $40k. I consider these sort of people scum. I don't know if they are assuaging their insecurities or what, but I don't know how you can look a youth in the eye and tell them to get a day job making web apps (for someone else) instead of going to Harvard for free for four years. Especially when the free tuition alone costs more than the offered salary. Scum.