Khoi Vinh is being a poor sport here. Criticism is an important part of the design world. In school we're taught to use criticism as another resource and learn from it. The design team at the New York Times could have learned a lot from this 'unsolicited' exercise. Instead, they chose to be offended.
That article you linked to contains a lot of unneeded and useless criticism of the Times that was only peripherally related to any actual design aspects of the site. When he goes off about ads, he's no longer talking about site redesign and is instead advocating that they change their business model.
He's certainly free to throw his $0.02 in along with the rest of the peanut gallery about how he thinks the newspaper industry should run their business - but it tarnishes what was supposed to be an interesting look at a web site redesign.
Perhaps more importantly, if I were current or former staff of NYT, I would have a hard time taking even the valid criticism found in Rutledge's post to heart, given that he implies exceptionally bad faith on the part of the Times staff. We all can cite a truly terrible online news design that would benefit from some of Rutledge's suggestions, but the focus on NYT seems like a oblique strategy to accuse the Times of something almost like yellow journalism, what with of the suggestion that opinion is shamefully placed in context with reportage, that popular news is pandering, etc.
"I will say this, though: unsolicited redesigns are terrific and fun and useful, and I hope designers never stop doing them. But as they do so, I also hope they remember it helps no one — least of all the author of the redesign — to assume the worst about the original source and the people who work hard to maintain and improve it, even though those efforts may seem imperfect from the outside. If you have good ideas and the talent to execute them and argue for them, the world will still sit up and pay attention even if you take care in your language and show respect to those who don’t see things quite the way you do."