The door to the shuttles is at the first stop of the tram, where you arrive to from previous level, if I remember correctly. It opens only after you've done the current mission objectives in that level. I also spent some time figuring out how to get it open, but now that you ask I also don't really remember what it was...
Only that the door on the middle stop has to open, I think. You need to do something on the third (furthest) tram stop from the start.
By the way, don't try to jump on the tram tracks from the roof of the tram. I did one time just out of curiosity...
