I think John was definitely in the wrong for attacking YC like that, especially on HN. I agree that definitely wasn't the way to promote MassChallenge.
I just recently applied to YC and it wasn't an easy decision. In fact I almost didn't apply for various reasons. Ultimately it was what the YC alumni have said about YC that made me decide to push forward. Getting $50k in cash is great, who wouldn't want that? But ultimately the odds of succeeding are dependent on so much more than whether you have enough cash to survive 3 to 6 months. Free doesn't make it better, it just makes it free.