That does seem the logical place for space trains is in an FTL universe with wormholes (or jump gates or star gates or whatever you want to call them). I was always sort of surprised that the Stargate shows never really explored the concept of trains, although Stargate: Atlantis got very, very close at a few points across its seasons.

(For what it may be worth, I had fun exploring the idea of trains in space in some short stories I wrote way back in high school and every now and then think about trying to write a longer space opera in such a setting, but I'm not very skilled a writer and day job needs must first.)