Bump, found an alternative solution:
appletv - Can I stream any video played with VLC player to Apple TV? - Ask Different
It uses AirFlick (Mac only) that allows you to watch anything on Apple tv by streaming the conversion in real time.
This way you don't have to wait hours to convert all your video files to mp4.
-The only disadvantage is that AirFlick is not for windows and I only have a laptop with Windows 7!
So I'm still looking for a better solution.