Musk's plan specifically calls for TSA-style security.
Your third point is nonresponsive to the argument. The ticket cost will reflect opex, but Musk's plan doesn't include it.
Yes, his per-mile tunnel cost estimates were extremely low.
Airplanes occasionally experience motion-sickness-inducing G's. Hyperloop pods will every trip. You'd at least want to know if the design is a vomit comet before you sank billions into it, would be the right point to make here.
The whole Hyperloop thing is back of the napkin wank.
I don't see how poorly chosen station locations invalidates the plan, though - those are just proposals, perhaps because it would be much more involved to estimate land prices within the city. It'll make it much more expensive than the figures they mention, but that doesn't make the overall concept much less interesting, since the land rights will almost certainly still be much cheaper than an on-the-ground solution like the current HSR that we seem to be willing to build.
One critique of Musk's plan pointed out that the Shinkansen trains were essentially a frivolous novelty until they were brought into city centers. The same thing was true of Southwest Airlines trying to service NYC from Idlewild. You have to terminate transit lines at places people want to go.
Also, the bar you're trying to set for critiquing the Hyperloop is too high. An argument against Musk's plan need not show that it's impossible to build. Rather, the bar is simply that an unproven new technology must have significantly better cost and performance characteristics than HSR. Nobody is going to drop many tens of billions of dollars to build this thing "just because".
The Hyperloop concept at least can point out the folly of pie-in-the-sky projections.
But the rest of it, the ridiculous route proposed, the estimates of right-of-ways and construction costs, and the comparison to the CA HSR plans that are going forward -- invited explicitly by Musk -- those parts of the plan are ipso facto nonsensical. That's why some people think it's just a tactical salvo of disinformation aimed at fragmenting what political support CA HSR has.
They invalidate the plan as an alternative to the HSR plan, which doesn't avoid the issue of connecting places people actually are to places people actually want to get, which is kind of an important part of any mass transit proposal.
WRT destructive disruptions, I believe there was a section dealing with sudden tube repressurization. If the failure mode is effective, it seems like an attack would be less destructive than one on a train, due to the smaller pod size.
If CapEx is much lower, and energy cost is lower, the ticket price should be lower, unless the maintenance cost is much higher (it may be due to exotic requirements, but it's not fair to say that what he's describing bears no relation to actual cost structure - it's just not complete).
No idea about the routing/tunneling estimates. Were his per-mile tunnel cost estimates much lower than normal?
The motion sickness complaint seems like it would have legs, since there won't be any view of the horizon - your eyes will be reporting a static environment outside your body, and your inner ear will be doing very much the opposite. Then again, planes experience turbulence and mild G forces and have the same characteristic for most passengers of not seeing the horizon. Maybe motion sickness was a much larger problem in the past, based on the presence of barf bags at every seat.