I have to admit that got me wondering! The best answer I could find I did get from another website so here is the URL http://uk.answers.yahoo.com/question/index?qid=20091014190803AA1R7dC
I think it comes from the early days of transport. One travelled 'on' a boat because only a rich person would have a cabin and the poor would sleep on deck. When coach travel was the norm only the rich would get 'in' the coach, the poorer ones would travel outside, so 'on' the coach. Buses are the descendants of the coach.
In addition in the early days of the railways poorer passengers travelled in open wagons so they were not really 'in' anything, whereas rich customers would have their personal carriages transported 'on' a wagon.
The use of 'on' is probably a left-over from these times. Thus by extension one gets on a plane or on a rocket. It is fairly obvious one is inside.
On the other hand, while the early cars were open-topped, by the time they became popular almost all had a roof. Because it is small, personal space, getting 'on' the car suggests climbing on the roof. So naturally one gets in the car.
Hope that helps.