I've been to hell and back working on this issue in the last month or so...I'm a huge fan of the Kuroshitsuji (Black Butler) anime, and would love to be able to watch episodes of it on my iPad in between my classes.
What I have: All 24 episodes softsubbed in 1080p .mkv format.
To save time from rambling, I'll say that I've tried just about every option I can find for getting the iPad-compatible .mp4 file to have the subtitles on there (softcoded), and I suspect the issue is that my iPad simply doesn't know how to understand the subtitles for some reason. I've had varying glitches ranging from the subtitles just not showing up, stopping at some points, or even getting a long and drawn out html-type coding language.
What are the options for hardcoding the subtitles to get it to work that way? Preferably I'd like to not lose too much quality in the process, as half the reason I'm doing this is to have awesome quality via the iPad, but I will sacrifice some if it means I can get this to finally work. File size isn't an issue.
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Have you gone to the App Store and gotten and installed the free VLC Player app? I don't have an iPad to test with, but it should be able to open your subtitles without having to do anything special. Note that you will have to open your MP4 file in Advanced mode to have the option to specify a subtitle file for it.