You're right that Clojure -> Java is an unfair comparison, but I do think there's significant differences between CoffeeScript as a language and Javascript. If you ignore the fact that the main implementation of CoffeeScript compiles down to Javascript, and look at them instead as two wholly distinct languages, I wouldn't consider them very closely related at all.

CoffeeScript has significantly different syntax from Javascript, different variable scoping rules, list comprehensions, a class system, and a whole lot of other features absent from Javascript. If you showed both languages to a programmer who wasn't aware that CoffeeScript compiled down to JavaScript, I'd guess that they wouldn't see much of a relationship between the languages at all.