There are a few different ways to do this.
1) On the Transcoding Settings tab, you can check the "Definitely disable subtitles" checkbox under Misc options
2) From the PS3 XMB, you can select the #Transcode folder, then select one of the different combinations of audio/subtitle options of transcoding there
3) If you have the main #Transcode# Folder enabled, you can globally disable subtitles from the PS3 XMB there as well.
Note: If you choose Option 1, you can still watch with subtitles selectively by going into the movie's #Transcode folder as well.