Because the land has vertical variations that you would have to work with, probably involving a lot of filling, bridging, and tunneling. The horizontal is just about planning the route. (Which of course has some restrictions as well, but not to the same extent.)
I was under the impression that a hyperloop would run mostly on pylons anyway, so just by varying their lengths it is possible to smooth the altitude however you want.
Agreed that pylons would let you filter out small changes, but in a place like Switzerland the land varies in height by a lot more than the average pylon.
