Public transportation etiquette?

Using public transportation lately, rather than an own car, has made me discover dimensions that I didn't know.

Yes, it's true: Comfort is sacrificed, Commuting times tend to be longer (except in the case of a subway) and traveling long distances becomes tricky. On the other hand, it is a cheap way to go from one place to another, and if the transportation systems in place are adequate, it doesn't get very difficult to get from point A to B.
There's a phenomenon that occurs in public transportation systems, more commonly in buses: people who travel alone, don't like to share the seat with strangers. Although people don't show their inconformity of having a perfect stranger sitting beside them, they aren't comfortable. Still, when the bus is full and there are few seats available, there's no choice.
I guess that there should exist some kind of public transportation etiquette that I'm not aware of. Think of the following situation: The bus is half full, there are no empty seats but almost all of them can be shared. So you sit on one of the seats, which you share with a stranger. A couple of stops after that, some passengers reach their destination and drop off the bus, leaving some empty seats. The traveler sitting next to you wasn't one of the passengers that left the bus, so you're still sharing the seat. What is more polite to do: to remain seated in the same spot, or to move to an empty seat?
As I see it, if you remain seated in the same seat, it will be mostly uncomfortable to the other person (and to you as well), especially when the other traveler is aware of the availability of empty seats. But, if you leave the seat to sit in another spot, it can be understood as if you dislike the person seating next to you, which is not polite to do. A big dilemma... any ideas on that?
Regardless of the existence or not of a public transportation etiquette, I'd encourage everyone to use public transportation, which helps to reduce the greenhouse gas emissions and the amount of traffic in the streets.