This system would seem very weak to criminals / terrorists / whatever firing bullets at it. It would be exceptionally difficult to track where the shot/s came from, and it would cause serious pressure problems.
Even if the pressure problems could be countered, a bullet hole is likely to leave a pretty ragged profile on the inside of the steel tube. The specification calls for the air bearing skis to ride 0.5 to 1.3mm off the tunnel wall. They'd need to be pretty robust to take hitting the ragged edge of a bullet hole at 700mph.
I think that a bullet hole in the type of tube that supports this much weight is unlikely. Oil pipeline tubes would typically be thinner (less weight to support) and the concept of a bullet piercing those tubes is unlikely.
I wonder - could you line the high-speed part of the tube with half an inch of soft wax or something similar? Then any dents or imperfections caused by bullets would rapidly be smoothed out again, and the damage to the skis would be minimized by vaporizing the wax you hit.
Aircraft sitting on the tarmac doesn't have to take off if it has been shot at. In the process of taking off could be more of a problem, I suppose. On the other hand, at least airports are a relatively small area to keep secure.
Airplanes leak so much air that a couple more half-inch holes would not affect overall integrity. Most control systems are implemented with redundancy, so taking out a control point would just failover to a backup. Occupants aside, there little such damage could do to an airplane; noting the occupants, worst case is a couple casualties, not loss of everyone on board. And, of course, you could simply choose to not take off.
As mhandley noted, Hyperloop might be more susceptible, as the concern is more like your airplane flying an inch off the ground and hitting a stationary large brick.
...which reminds me of an old analogy: Back when large-capacity (ooh! 10MB!) hard drives were becoming common, I recall hearing the comparison that the read head was akin to a 747 traveling Mach 3 just 1 inch off the ground. Perhaps Elon wondered how this might work in real life, and so came up with Hyperloop.
Aircraft are actually supposed to leak air. In non-bleedless aircraft, the engine compressors pressurize air to be used in the A/C unit, which then sends all the pressurized air throughout the cabin. To prevent excess pressure buildup, valves are opened partially most of the flight with a veinlike network of tubes venting air to the exterior of the aircraft.
Of course, if any damage occurred on the ground, this would be a non-issue entirely as the aircraft wouldn't be pressurized at all.
