Well actually either can work, but since you are describing an action (standing) "in" sounds better...especially since you are not inside the bus. If you are just saying that he is on the bus, "on" works best.
Nonetheless, here is a rule of thumb for this:
For vehicles, anything considered to have a large floor space is ON and a small floor space is IN. Large floor spaces are considered platforms, small floors are considered containers.
Therefore it's in a car, in a small boat, in a helicopter, in a rocket, in a hot air balloon, in a small plane (think of a an old biplane).
But we say on a train, on a ship, on the space shuttle, etc.
When the platform has no walls (i.e. it is not an enclosure) we say on, too. So it's on a stage, on a table, on a horse, on a bike, on a skateboard. If we confuse on with in in these cases the visual image becomes very different: in a horse means you physically enter the horse's body, for example.
Because the language is dynamic, and because it is old, some exceptions will emerge but this is the basic rule. Some regional differences also exist, and sometimes in and on have slightly different uses even for the same transport, but if you stick to the general rule you'll rarely be wrong. Once you begin to visualize objects as platforms or surfaces, on becomes logical too for other kinds of objects: on a screen, on paper, on a page and so on.
In a car, on the car roof.
On a chair (no walls), in an armchair (three walls but note some people say on because it's a chair), on a sofa (larger surface).