I'm sure some people will still fly, but all the airlines would go out of business, so it won't matter. Perhaps we can go back to sailing caravelles across the ocean.
Well, there's a game called FTL (very good Roguelike with real-time ship-to-ship combat) [0] that has teleporting bombs as a distinct class of weapons... So of course, it's not hard to imagine that matter teleporters could and eventually will be used to great offensive and invasive effects, depending what the laws of physics allow.