Even in case of catastrophic damage to the track, a Transrapid would, at worst just derail (and in most cases, it'd drop on the track and probably simply stop). In case of catastrophic damage to a vacuum tube system, you're dealing with a violent, devastating implosion that would most likely total the entire track and obliterate whatever's inside.
Ah, I also forgot to mention that you can't run multiple trains inside a single tube using this system. Overall, it seems that it'd be more suited for urban communication than for long distances. Metro, for example, wouldn't mind only running one car on a single line (at least if it's short) and an underground tube would've much lower risk of being breached. It could also be controlled from a central pump station inside the city, somewhat simplifying the system.