Do they? Seeing as how tech companies aren't allowed to divulge they're the NSA's bitches and have to hand over all their data, I don't think that public services like trains (or electricity, etc) are allowed to shut down their services if they disagree with the government's imposed security measures. Pretty sure there's sections in the anti-terrorism laws that say companies need to comply when the government brings in counter-terrorism measures like searches and the like.

Besides, they'd probably comply willingly. The airline companies and airports do; hijackings just ain't good for business.