I currently have my Apple TV hooked up directly to my Receiver (HDMI 4). The receiver is hooekd up to the TV so all video and audio goes through it.
The video plays fine and any audio other than 5.1 ac3 plays fine through my receiver speakers....but for some reason it has issues with the 5.1 ac3. If I start a movie using the set up above, with dolby digital set to on and an ac3 5.1 and aac 2 channel audio set up on the streamed apple tv file then the movie won't start (no video, no sound, nothing). If I turn dolby digital from on to off in the apple tv settings then it will work using the aac 2 channel audio.
I decided to try it out with an opitcal cable because of the below article.
http://techtips.salon.com/hdmi-vs-optical-cable-21243.html
Audio Limitations
Optical cables support surround sound with up to 5.1 channels, while HDMI supports Dolby Digital Plus, DTS HD and TrueHD formats. While most television programming is broadcast in surround sound, many Blu-ray discs offer enhanced sound quality. If you're an avid Blu-ray watcher and want the best possible sound, HDMI is the best choice for you.