Yes, I understand what you mean and when I wrote this I knew that someone would comment on it :)

This is how I see it:

Pure JavaScript + JQuery = Very easy to get started but very hard to maintain when the code base grows if you don't know JavaScript very well.

CoffeeScript + JQuery + Backbone.js = Harder to get started but the code becomes easier to maintain when the codebase is big.

I know that JQuery is not about organizing code.