It wouldn't be two separate tubes but one LOOPED tube. Thus why it's called a HyperLOOP. It may look like two tubes to you, but a Mobius strip looks like it has two sides yet it doesn't.
Protecting the pylons? Known science. After that bridge collapse in Tampa (which involved impact by a SHIP), people are well aware of the need of buffer zones and better impact-deflecting column designs (think a circular column with a parabolic base—anything running into it should be deflected away). If they can keep SHIPS from colliding with support columns, a truck shouldn't be that challenging.
As for businesses along the way, they may not get a say. The loop's being built on already-allocated right of way: along the I-5 corridor for the most part, switching to I-80 for the Bay Bridge run. All that land's ALREADY owned by the state, so two words: they lose.
As for flying cars, reliability keeps them from being practical (Breakdown in midair? *shudder*). Teleportation? I think the Uncertainty Principle gets in the way. And status quo is unacceptable (observe the typical LA rush hour). So you're basically in gold rush territory: boom or bust, with nothing in between left for you.