He rightly draws the analogy between jQuery and JS. I spend a lot of my time working on jQuery core, and we have definitely seen the phenomenon described in that blog. Five years ago when jQuery was created, just about every web developer knew JS quite well and understood the quirks of every browser and JS implementation. Now, they just assume that if something doesn't work consistently in IE6 then it must be a jQuery bug, because you know, jQuery is cross browser. People are now programming in jQuery and have given up on JavaScript.
If you're a CoffeeScript pioneer you don't see this. You already know the hard and ugly JS things that CS makes easy and beautiful, just like the early jQuery adopters. A few years from now if browsers haven't created native CS implementations but CS is popular, novice programmers will be dealing with the same jQuery-vs-JS dilemma. For example, programmers with weak JS skills will write CS and be baffled by the errors thrown from the bowels of the JS code they are forced to debug.