This is not really a fair comparison - even without a congestion toll, people have to pay to drive on a road. They need to buy the car, pay for its maintenance, fill it with gas, pay for insurance, pay annual registration fees to help maintain the roads. Presumably some of the money from buying a train ticket goes into doing the equivalent things: purchasing and maintaining the trains, etc.

Not saying the implicit subsidies/taxes on each mode of transport is equal, but it doesn't seem to be as simple as 'one is paid and the other is free'.