Question: what is the difference between on the bus and in the bus?
Answer: It is much more commonly used than 'in the bus'. The use of 'on' does NOT imply that the person is on the roof. Basically, if the speaker is taking a long trip by bus, that person is said to be 'on the bus' during the entire trip. When a person is boarding a bus, we'd typically say the person is getting 'on' a bus.