This statement was made in comparison to merb, which succeeded in getting more mindshare than the other 'Rails competitors.' This was largely because merb attempted to do much the same things that Rails was trying to do, but to do them in a much better way.
He was indirectly positive about Sinatra throughout his talk, and when covering router changes, kept describing how you could mount Sinatra applications inside of your Rails3 app.
The "prototype sucks comment" was made along with a very tongue-in-cheek "everyone will move to jquery" comment. He was laughing when he said it, and I got the impression that he was simply making a joke as the author of jquery.
He never once said anyone was stupid. Actually, that's not entirely true, he was pretty critical about some of the code found in Rails 2.x. He backed his criticism up by showing the code, and I certainly didn't think he was out of line.