Just about everything is a pain point when using JavaScript or when dealing with the DOM. So it's understandable, although maybe not a good idea, why so many people don't separate JavaScript and libraries like jQuery, MooToo, or YUI.

Such a combination is essentially needed merely to bring JavaScript up to a minimal level of usability. We generally don't find this to be the case with other, more sensible languages, which is why it seems so odd. C, C++, Java, C# and Python implementations come with a sensible language and a rich standard library. Developers using them don't need to bring their own standard library just to get a basic level of functionality.