I don't understand what you're getting at. Why do new "protocols" need to be folded into the web?

The web can't ever be as well-managed and patched as Linux is. The web doesn't have a pre-defined scope. It's more like a transport layer for content and other services. And I'd like to see it stay that way; companies will compete and innovate way faster than any small standards committee or group of maintainers will.