The safety reason is a big reason why I'm going with the underground tubes between LA and SF.
Engine failure doesn't kill people, because you can typically glide to a landing. Speculatively, if you got your glide ratio perfect and launched high enough, you might not need an engine to get between LA and SF.
But yeah, flight is comparatively one of the safest ways to travel. But, in principle, it is still quite risky. A lot has to go right for an aircraft to successfully take off, fly, and land. Air speed must be maintained, the engines must remain mechanically sound, landing gear must be operating correctly, hydraulics on the wing and tail flaps must be operating, the pilot must be competent and alert. Countless systems must be working correctly. Any one of these things going wrong can result in mass casualties. Statistically our standards of operation are so high that flight is effectively safer than the automobile or trains or even lightning, as the article points out. But 1 in 12 million is still far from the effective 100% safety that Musk is promising for hyperloop.
And I keep hearing people trying to apply Hyperloop to coast-to-coast travel, but I don't recall Elon every saying anything about that long of a distance. In fact I recall him specifically talking about "the right city pairs", which implies some kind of distance limit.
The $6 billion cost seems too good to be true for any transportation system that would require significant land acquisition. California is set to spend some $60 billion on a train between these cities, and most of that cost is for right-of-way.