Well yeah, but MKV usually contains either XviD/DivX or (more frequently) h.264. I was simpifying my statement. Anyway, your media player can't just run the subtitle file when playing the video? Can you use VLC?
VLC is what I use to watch pretty much any fansubbed anime. That's not the problem, though. I've not found any sort of option that allows VLC to run subtitle files separately from the video/audio.
*shrug* Dunno. I'm a very lazy dude, I didn't enjoy compiling a Matroska file with converted video, and I'd rather just have things done for me. If someone released an .avi version of the Animal Crossing movie with subtitles, or an .mkv version of the movie with the video codec being DivX/XviD instead of h.264, I'd rather just simply download that instead.