You don't have to worry about cows wandering into oncoming vehicles like you do with cars and trains. It's also harder for non-determined people with malicious intent to interfere with operations.
A determined attacker can, of course, scale pylons. But you don't have to worry about stuff like kids lobbing bricks from overpasses, or people pushing others onto subway tracks.
On the other hand even with a recommendation to use something similar to TSA doing something similar to airport security, his response plan to a terrorist attac--, er, a "human related incident" is basically to say that the system will have redundant power and vacuum pumps.
I suppose this isn't his area of expertise and so it's better to say little, but this is the kind of thing people are going to worry about before they board a small tube hurtling at 700 mph while 100 feet above the ground.
For instance, does a HRI impact his plan for rapidly handling luggage pods at all? Just one thing to think about...
The big benefit of hyperloops over planes would all depend on how quickly you could brake those pods and re-pressurize the tube to let people escape. Because that's something you definitely can't do on a plane and it governs most of our thinking about them - if anything happens, you're possibly over an hour from being able to land anywhere and no one is able to get off quickly.
Oh, bus-bombing happens; mostly in the middle-east, but it did happen in London once. You can google it.
I also expect that an explosion inside a depressurised pipe would shut the whole thing down in a way that an explosion above a road surface would not.
I was worried this was going to be some pie-in-the-sky idea that was nebulous on a lot of basic details with quite a bit of "we can figure that out later".
Sure, they put a lot of theoretical analysis into it, but its still pretty pie-in-the-sky. From the last page, note that
The authors recognize the need for additional work,
including but not limited to:
1. More expansion on the control mechanism for
Hyperloop capsules, including attitude thruster or
control moment gyros.
2. Detailed station designs with loading and unloading
of both passenger and passenger plus vehicle
versions of the Hyperloop capsules.
3. Trades comparing the costs and benefits of
Hyperloop with more conventional magnetic
levitation systems.
4. Sub-scale testing based on a further optimized
design to demonstrate the physics of Hyperloop.
It's not a current competitor to high-speed rail, its more in the position that high-speed rail was in in the 1930s.
I think, if anything, safety aspects haven't been sufficiently explored in the pdf. I'm quite happy to believe it's safer than other modes of transport, but I wouldn't be too quick to overstate it. Also, if anyone can explain what "Tubes located on pylons would limit access to the critical elements of the system." is meant to mean in §4.5.6 I'd be grateful...