I am currently working on two projects written predominantly in CoffeeScript, and I completely agree with your original post. It is a mistake to think of CoffeeScript as simply another Javascript, and it is a mistake to make the assumption that people that are comfortable with Javascript will be comfortable within a CoffeeScript project.
CoffeeScript is more than just Javascript with a small sprinkling of syntactic sugar. There is a definite learning curve between Javascript and CoffeeScript. List comprehensions, extended regular expressions, and splats - these are just a few of the things that make up that learning curve. The changes in variable scoping that CoffeeScript makes is another.
I think that perhaps the best practice for publishing a CoffeeScript project should probably be to append a .coffee to the name rather than the usual .js. This would go a long way towards eliminating the kind of misunderstanding that you refer to in your OP.
A side note, am I the only one that has noticed an increase in downvote-readiness here lately?
That's why I down voted you. Is a JS compiler beneath you? Fine. Then post about that. Don't try to slip it into a veiled complaint about title accuracy.
If I can't fork and contribute to the project in javascript, but instead have to set up my environment for coffee script to contribute, then it's not javascript.
This isn't just about readability and comprehension, it's about contribution as well.
If the compiled javascript is bundled in there and I can read it, fair enough. If you can't accept patches and code contributions in javascript, then that's not javascript.
My comment is civil and explannatory. You may not like my sentiments, but down votes are not intended for unpopularity. Not only that, but in this case, my comment serves to reinforce the standards of HN regarding mis-titling of links and it is being downvoted.
A house divided against itself cannot stand.