Why is it that in English we can say ( On the bus or in the bus, yet can't be on the car! but In the car...)
What is the difference
That is some question!
Normally while travelling you say on the bus, or in a car. That's the way it is.
If you wanted to say in the bus, or on a car, then the first one would imply an action taken by someone not involved in travelling, say firefighters trying to get into a bus to distinguish a fire in it; the second one would only mean that you are physically on the roof of a car.