Yeah a lot of people conflate JavaScript with the DOM because the only place most people see js is in a browser where one of its major purposes is manipulating the DOM. Admittedly the DOM has had a checkered past.
But js's story is much bigger than that.
Also I would argue that jQuery just uses a different set of the language's syntax than many programmers would ever encounter just coming from the c-style languages.
It forces you to use closures before many programmers actually know what one is. Some never do or never need to.
Further to this, a lot of the problems one has with the DOM and browser differences are a non issue on the server where you tend to work with much more mature engines, such as Rhino or V8.
Our only minor gripe at Akshell (http://www.akshell.com), which incidentally the original poster should check out, is the hype around asynchronous I/O on the server.
It appears to be a case of premature optimization and tends to throw off new developers just starting out with the language. Since ease of development is our top priority, Akshell defaults to a synchronous model.
Also, jQuery doesn't "fix" JavaScript, it "fixes" the DOM. I.e. jQuery and many other libraries, have little to no use for programming games (shameless plug: e.g. with Impact[2]) or server side stuff. And some of jQuery's ideas have already been implemented natively in browsers[3].
JavaScript is extremely flexible and allows implementations of other languages like Coffescript with relative ease. I don't see a problem with "fragmentation"; it drives innovation.
[1] https://developer.mozilla.org/en/JavaScript/Strict_mode
[2] http://impactjs.com/
[3] https://developer.mozilla.org/en/DOM/document.querySelectorA...