CoffeeScript is only kinda "another language." It's very intentionally designed to map closely to JavaScript. Try it with an actual independent language like Python, Ruby or Haskell and you'll have more trouble.
Yea, Coffeescript incurs no penalty because it's so close to Javascript, but therefore it doesn't fix Javascript's flaws either. Coffeescript still doesn't have proper lexical scoping and it doesn't have a good standard library.
CoffeeScript incurs no penalty when compiling to Javascript; in fact, in many cases it's faster than handwritten code.