Well, airplanes are a considerable distance up in the sky and incredibly difficult to reach. It's why the vast majority of plane-related "badness" happens shortly after takeoff or shortly before landing. Any land-based rail vacuum tunnel would not be protected in this way. An underwater one would be to an extent- I suppose it depends how deep it goes. But it's still a lot easier to drop something (say, a bomb) into water and let it sink than it is to fire it into the air and hit a plane.