Maybe, but I'm not convinced. It doesn't matter if you're flying or not, if you're traveling at supersonic speeds and you run into anything, even if you hit the ground from a height of 10cm, it's going to be a bad time. Also, if you're traveling that fast it is magnificently easy to gain a dangerous amount of altitude quickly just by having your vehicle rotate and hit a favorable angle of attack. Just look at how dangerous and dramatic crashes in formula 1 or nascar are, and those vehicles are on the ground, and traveling at maybe 1/5th as fast as a hyperloop vehicle would (and with 1/25th as much kinetic energy).

I'm convinced there either must be some other factor at play or Musk must have worded his statements stronger than is warranted.