If you are converting your movie straight off a dvd try using Handbrake. It is a very powerful program and gives you access to about everything. Subtitles, chapter markers, and how you want to convert it. Go to macupdate[dot]com and search for Handbrake
Letting us know what software you are using would be helpful...
I'm sure there is just a setting for the subtitles buried somewhere that you are missing. Maybe look out for different terminology, i.e. subpicture or captions?