Imagine you live on the outskirts and you commute to work by bus. The bus's route is from A to B and back. You live between A and B, which means buses are traveling either towards the city center or towards the outskirts in a given moment. 'in' in 'in bus' conventionally describes buses that propagate towards the in(side) of the city, towards the center. 'in' can denote not only the inside of a city, but the inside of something else too. I just picked out an example.