1) Testing the hypothesis that university is bad
2) Testing the hypothesis that university is not worth the cost for the vast majority of people
What the Fellowship might plausibly be doing:
1) Testing the hypothesis that university is not worth the cost for people like the Thiel fellows
The actual motivation of the Fellowship, which is all over the press and has been related to me by Thiel Foundation workers, is that students with great potential accumulate tons of student loan debt in college and subsequently, instead of taking on projects that might actually help the world, are financially pressured into working at hedge funds and the like. The Fellowship is offered to these students as a two year break to attempt these projects supported by 100K for living expenses and, crucially, extensive mentorship.
Again, the point is not to discredit universities, but to keep talented kids away from hedge funds (ironic coming from Thiel but there you have it).
Edit: Also note that a failure of the Thiel Fellowship project does not disprove the education bubble in general, since it only applies to a very small group of people.