The AppleTV is a bit short on fonts. Out of the box you have choice of Apple Gothic, Aqua Kana, or Lucida Grande. This can cause problems when viewing subtitles.
Quicktime text tracks that specify other fonts won't render properly, and codecs used to render other varieties of subtitle track may fail for similar reasons.
To fix this, either install the missing font (usually Helvetica) or update your text tracks to use one of the existing fonts.
I have had success with using .srt subtitle files with Divx movies. Subtitle files worked out of the box using ATVFiles and Perian 1.02 Beta. However, the default font size is so small that it is nearly unreadable, even on 50+ inch HDTVs. The same setup on a normal Mac running the same version of Perian results in large text headings. The reason for the size difference is because Perian looks for the font Helvetica, which is not installed on AppleTV.
To remedy this, copy the file "/System/Library/Fonts/Helvetica.otf" to the same location on your ATV. After uploading this file subtitles should be nice and clear.
Note: This issue will likely be fixed in future versions of Perian. Please see this ticket.