Yes, I think "in" would hardly ever be used with a train/bus and various other large, collective vehicles. If you really want to stress the idea of being enclosed by the walls of the vehicle, you can use inside: e.g. he was trapped inside the train.
Generally use on with large collective vehicles-- on the bus/plane/train/tram/boat/ship/ferry-- or ones where you're physically on top of the vehicle-- on his scooter/bike/moped; use in with smaller/private vehicles that enclose you: in the car/van/helicopter.