go to school by bus 表示乘公汽去学校
go to school in the bus 表示乘公汽去学校,要用in 这是固定搭配（bus是特指的）
两个词组意思一样,但用法不同.
原错句：The bus by which he goes to school every day is a red one..
原对句：The bus in which he goes to school every day is a red one.
由句中The bus 、a red one知道该bus是特指的,所以用in
理由就这样,ok?