At the moment, the only way to get subtitles to show up on the TV through Apple TV is to use AirPlay mirroring. That means, everything from your device is mirrored onto the TV just as it is.
Unfortunately, you might have to adjust the resolution on your TV to enlarge the image as the resolution of your TV is likely to be different than your mobile device.
The mirroring function is an iOS function that we have little control over. We're trying to figure out a better way to manage this, so stay tuned.
For more information, please visit Apple's support page on AirPlay at http://support.apple.com/kb/HT5209