I'm not particularly sold on CoffeeScript, however this article seems to imply we'll someday have to maintain the generated files? As long as you keep the source near the generated files (which should be easy with version control -- you shouldn't even be checking in the generated source, in my opinion), I don't see the problem.
I'm somewhat unsure of the long term cost to benefit ratio of using Coffeescript. You are basically getting some syntactic sugar in exchange for the cost of learning new syntax and complicating your build and debug procedures.
I'm trying coffee on a relatively small project with only a few developers. So far I'm happy with the tradeoff. I keep my Coffeescript simple so the Javascript is almost exactly what I would write by hand.
Agreed, I usually .gitignore the generated JavaScript. Though sometimes it is useful to also provide JS in the repository, so people checking out the repo can immediately have running examples.
