There's everything wrong with that. There are huge benefits to handling the internet as a linked graph of documents and resources. Try writing a site that loads all its content via Javascript and see how well you rank in Google.

I have nothing against the existence of web applications, as long as it's recognized that they have a fundamentally different nature and purpose than a web page. The W3C doesn't always make decisions that are right for everybody, but they've done a pretty decent job of preserving the ideal of a document/resource-centric web. And it's important that it stays that way.