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.

5 times the speed = 25 times the kinetic energy (per kg). And that is for the 'slow' one. At 4000mph, it is more like 64 times. And yes, this only talks of a 6-person capsule, but I think you would need to send quite a few of them through that tube to make it economically feasible. You wouldn't need to bring explosives to destroy the tunnel. Just have enough to have a 10 kg or so part drop from one of those capsules.