I've seen some genuinely horrible Javascript. Like, stuff that so terribly abuses the language without any comprehension whatsoever of closures or context binding and only works because the author got stupidly lucky and/or abused globals so badly that the code was effectively one giant function. In both cases, bad developers writing bad code are going to produce unmaintainable messes. Doesn't mean that the language should be avoided. Garbage in, garbage out.
nasty: https://github.com/jashkenas/coffee-script/blob/master/src/r...
nasty: https://github.com/jashkenas/coffee-script/blob/master/src/o...
nasty: https://github.com/jashkenas/coffee-script/blob/master/src/c...
sexy: https://github.com/jashkenas/coffee-script/blob/master/src/g...
nasty: https://github.com/mirrors/gcc/blob/master/gcc/c-family/c-co...
nasty: https://github.com/mirrors/gcc/blob/master/gcc/c-family/c-le...
But you get the idea. I'm merely pointing out that compilers are tricky and complicated beasts. And especially in the rewriter CS has to jump through hoops to disambiguate.
Plus, if you don't like it at all, just don't use it and quit complaining. :)
You could say "don't take that job", but I think the point of the article is to make it clear that CoffeeScript is not an unvarnished win, and that choosing to use it will result in otherwise qualified people taking your advice and not wanting to work on your project.