IIRC, the choice was between no trains and a train. I think a lot of people voted for it so they had a cheaper alternative than planes and a less time/effort intensive alternative than driving.
> If you don't want to be searched at the train station, you have the freedom to not ride the train.
http://www.bbc.co.uk/news/world-us-canada-23677205
I'm sure there some contingency has been thought of, unfortunately it's just the world we live in these days :(
I responded to concern over the Hyperloop shutting down for hours whilst the damage is repaired.
And, if someone fired a few pot shots into a taxing A380 at LAX, I have to imagine that the whole place would be shut down for a few hours.
As mhandley noted, Hyperloop might be more susceptible, as the concern is more like your airplane flying an inch off the ground and hitting a stationary large brick.
...which reminds me of an old analogy: Back when large-capacity (ooh! 10MB!) hard drives were becoming common, I recall hearing the comparison that the read head was akin to a 747 traveling Mach 3 just 1 inch off the ground. Perhaps Elon wondered how this might work in real life, and so came up with Hyperloop.
Of course, if any damage occurred on the ground, this would be a non-issue entirely as the aircraft wouldn't be pressurized at all.
Most likely safer than a train.
Remember a big part of TSA isn't to protect the people on the planes, but to protect other people from the planes themselves. It's pretty hard to weaponize a vehicle that's stuck inside a tube or on rails.