It's also easier to stop a train, get off a train, or prevent collateral damage in case of malice/accident. Survivors are also a lot more likely if there is an accident, mostly because of gravity.
Assuming passenger trains of course. I think a freight hijacking is far more likely. The danger posed by a hijacked freight are evident from the huge numbers of lives lost from exploding petroleum trains over the past few decades.
TSA isn't really for hijack protection, that was solved quite quickly after 9/11 with effectively impenetrable cockpits.
It's really for preventing destruction of the plane itself. A large bomb on a train underground could cause way casualties, which is why the strictness of the TSA is puzzling.
(That doesn't excuse the TSA's security theater, obviously.)