I can see how you can interpret that sentence in isolation as talking about websites in general. In fact, I'm not sure why I didn't interpret it that way first, too, but I interpreted it as talking about particular websites. In other words, it's not about HTTP vs FTP or IRC, but e.g. Facebook vs Twitter or StackOverflow or allrecipes.com.

I probably read it like that because of his following paragraph, which talks about how particular websites have this "walled garden" feel and how some people don't move much away from them to the point that they consider these particular websites to be the whole internet. Since the topic of this subthread is about how people of the internet have less in common now that it's become mainstream, that interpretation seemed to contribute better by raising the point that, to many people whose interpretation of the internet is a "walled garden" like Facebook, their "internet" has not become mainstream, or at least not on the level of the "internet data connection" or the real internet.