There's a world of difference between fully supporting something and making it your default. Making newcomers jump through hoops to get regular javascript instead of CS (another language in which they may not be familiar) just seems like a poorly thought out plan. As someone pointed out in the GitHub comments; this is just like making HAML and SASS the defaults over HTML & CSS.
I'm not saying anything negative about these libraries; I'm certainly not an authority on them and can't speak to their effectiveness. However, the net result of a default change such as this one is reduced accessibility to newcomers.
Of course, if I'm reading it wrong and this is really just adding support for CoffeeScript to Rails, then disregard everything I just said. :)
Edit: well, don't disregard it--remember it for the future!