I've been trying to figure it out too. My Apple TV 2 isn't displaying all the subtitles for The Girl with the Dragon Tattoo, even though all the subtitles display correctly in Quicktime/VLC.
Biggest pet peve about the Apple tv is subtitle support. Handbrake can burn in SSA subs but it has many font issues with text over lapping and timing issues.
I am prepared to give the Apple TV away and move to a PC and XBMC since a lot of things i watch a subbed.