I agree with you that YC and things like it are not a real threat to higher education, but not because of the (relative) lack of success in the companies that have gone through them. The question that matters is which of the two produces people with skills more widely valuable to society. That is a harder question to get hard data on, but it seems clear to me that the skills gained in building a (usually technology-focused) startup, while valuable, are extremely narrow in scope when compared with the aggregate of all the different skills different people gain in college.
You make an interesting point, but keep in mind that individuals attend university because of what they believe it will do for them as individuals, not because they believe it will benefit society. University is promoted as and widely perceived to be the key to a middle class life. That's why many folks are willing to take on outsize debt to attend university (or send their children), and how politicians justify treating higher education as an entitlement worth of massive subsidy.
While the university value proposition has become less compelling because of rising costs and a harsh economy, Y Combinator and programs like it will never come close to establishing the same type of value proposition for a simple reason: most young people who start businesses with no capital of their own and no domain expertise are not going to be successful.
