Rail has the advantage that they can just shut down commerce across the country for a few days if the government does anything they don't like, and they have the balls to do it.

Well, Amtrak doesn't have that power, and I doubt the freight companies care what TSA does with Amtrak.

Amtrak doesn't actually own the rails (except in the northeast, I think). That's where we're talking about here, but in Seattle BNSF owns the track so TSA would have to deal with them.

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.