mkvmerge -o output.mkv -atrack !2 input.mkv
But I wasn't able to get the exclamation mart (meaning DON'T copy this track) to work. For some reason I kept getting "track not found" message. This should work with --vtrack or --strack (subtitle) or whatever.
Fortunately, I wanted to remove all the subtitles from my files, so I used the following instead:
mkvmerge -o output.mkv --no-subtitles input.mkv
If you only want to do this on one file, the mkvmergeGUI is fast and easy, but if you want to do it on a whole directory of files, you want to use this at the command line in a "For Loop," like so:
for i in *mkv; do mkvmerge -o ./newfiles/`basename "$i" mkv`.mkv --no-subtitles "$i" ; done
This will remove all subtitle tracks from all MKV files in the current folder, then put the new files in a previously-created sub-folder named "newfiles".