Fair enough. However, I think you are underestimating the size of explosion that it would take to seriously damage something like this. Engineers will definitely think about things like earthquakes and accidental (or intentional) collisions (such as a truck hitting a support pillar).
I also think you are overestimating the number of terrorists running around with RPGs.
EDIT: Of course, when all is said and done, the additional engineering requirements to make it safe may also make it economically unfeasible, in which case, your original point about the dangers would be essentially correct.
Unfortunately vacuum tubes are very vulnerable, they would have to be ridiculously overdesigned to take even a small explosion or a truck.
Terrorist with an RPG is just an example, it can be anything - a drone with C4, somebody throwing a long string of burning thermite, or just a gasoline canister set on fire.
All of these things can cause the same loss of life on any current mass transportation system.
This reminds me of the people who were very vocal about automated cars needing to be perfect before they could replace human drivers. They seem to have quieted down as the technology gets closer to actual deployment. I suppose that will also be the case here if the hyperloop becomes reality.
Not the same loss of life. A large rapture will propagate through the hole vacuum tube at the speed of sound, likely killing everyone, not just one pod.
Also it's a much easier target. Planes are only reachable to the terrorists during takeoffs/landings. And even then, it's not exactly easy to hit a plane moving at 300mph with an RPG/truck/drone.
The rest of your argument about automated cars is the classic example of straw man.
I also think you are overestimating the number of terrorists running around with RPGs.
EDIT: Of course, when all is said and done, the additional engineering requirements to make it safe may also make it economically unfeasible, in which case, your original point about the dangers would be essentially correct.