Travel by train, etc, not with the train, etc
Don't say:
He travelled with the train yesterday.
Say:
He travelled by train yesterday.
Note:
We Say: by train, by boat, by plane, by bike; also, by land, by sea, by air, by bus; in a bus or on a bus; by car or in a car, by taxi or in a taxi; on horse-back, on a donkey, on a bicycle; on foot.