The Apple TV format does not support AC3 5.1 encoded files.
Movies played on a PC with surround sound require tighter compression and an audio format that is backward compatible with standard stereo receivers.
AC3 isn't really a good codec for surround sound in movie files because it uses a fixed bit rate. The newer AAC--developed by Dolby to succeed AC3--also supports 5.1 (or more) channels of audio, and delivers better quality at the same bitrate.
AC3 is a audio format that is suited to DVD, just as MPEG-2 is similarly designed for DVD's on the video side.
Digital Media Converter Pro will convert your videos to a MPEG-4 (H.264/AVC video and AAC audio) specifically designed to work on Apple TV with high quality video and audio.