The TSA wants to expand into trains, buses and car searches. But in the case of Amtrak perhaps they went too far and too fast. The main reason I can see for search people after they get off a train is to create a climate of fear, not safety on the journey already completed. Perhaps there is hope for our Fourth Amendment rights...
Attacks on passengers' civil rights is one of the most unpleasant parts of flying. But the cancer is spreading to buses and trains. The TSA's Visible Intermodal Protection and Response (VIPR) teams "detain and search citizens at railroad stations, bus stations, ferries, car tunnels, ports, subways, truck weigh stations, rest areas, and special events." According to the TSA News Blog: "VIPR teams periodically descend on transportation hubs to conduct "random" searches, as they did in [various major cities]; and perhaps most notoriously, in Savannah, Georgia, where train passengers were separated from their luggage and body-searched after they got off the train. Amtrak Police Chief John O'Connor hit the roof when he found out and forbade the agency from ever setting foot in an Amtrak station without permission again
From http://aviationjustice.org/2011/12/05/tsa-american-trains-and-buses/