"I thought the article was fairly straight forward until I got to the point you quoted. It's as if the attitude is that YC picks all the great startups and non-YC companies are second-rate throw aways that are destined to fail."

Huh?! That's putting a lot of words into the author's mouth. These companies may or may not be great, but it's true that they are not vetted in any way other than they've heard of YC and took some time to fill out an app. I hope they all succeed, but it doesn't seem out of line to suggest that companies NOT accepted/interviewed by YC aren't inherently fundworthy when compared to those that are.