The linked article says it's desirable to do this without requiring a right-of-way or moving people out of their homes. So that puts the tube below ground level -- well below.
Let's say an evacuated tube, below ground level, in California, between San Francisco and Los Angeles. This really isn't going to work, because (all other considerations aside) the route crosses any number of known geological faults that are in constant relative motion -- some creep past each other, some wait and then periodically move all at once in an earthquake. You can't build a subsurface tube that crosses geological faults.
I don't think this is a practical idea. But it's a nice one in principle.
Except for the small problem that Elon said it's not an evacuated tube: https://twitter.com/elonmusk/status/224406502188916739
TL;DR Build a rail with a high-velocity rotor inside that inertially supports it above the atmosphere. Essentially it's a space fountain with two base stations instead of one.
So yes there's a pathway, but since it's not on the ground it requires no right-of-way.
>However, while the Court rejected the unlimited reach above and below the earth described in the common law doctrine, it also ruled that, "if the landowner is to have full enjoyment of the land, he must have exclusive control of the immediate reaches of the enveloping atmosphere." Without defining a specific limit, the Court stated that flights over the land could be considered a violation of the Takings Clause if they led to "a direct and immediate interference with the enjoyment and use of the land."
Would a hyperloop cause direct and immediate interference with the enjoyment and use of the land? It might if it failed!