just checked the specs on apple.com.za for the last version. don't think FLAC was included.
Apple TV 3
Audio Formats
HE‑AAC (V1), AAC (16 to 320 Kbps), protected AAC (from iTunes Store), MP3 (16 to 320 Kbps), MP3 VBR, Apple Lossless, AIFF and WAV; Dolby Digital 5.1 and Dolby Digital Plus 7.1...