And to make this necessary encroachment somewhat more tolerable, we should at least try to delay it as long as possible: When on a lightly crowded bus or train, don't sit down beside someone else until it's absolutely necessary.
This relates quite closely to the concept of urinal etiquette, which provides guidelines for basically the same problem that dudes have at a bank of urinals. For those readers without funhoses, I'll explain: Dudes don't like peeing beside other dudes, and will position themselves at a bank of urinals to maximize the amount of space between everyone. There are quizzes you can take to learn the etiquette, but for transit-related circumstances, the shorthand works really well: Always go for an isolated seat before you sit down beside someone.
Here, green means good. Sitting in a red seat is an act of open hostility, about the equivalent of twisting the head off a doll while staring at him unblinkingly, humming "Hakuna Matata."
A side note: Experts agree that you get Bonus Bus Points if you're willing to move to an empty space when one opens up. Yes, this "feels weird" -- you're going to worry what the person you're moving away from is thinking. "Do I smell?" is one obvious possibility. "Is that guy racist against stinky people?" is another. But don't worry about it; that weird feeling passes quickly, as everyone involved enjoys the extra space they've just acquired. Don't try to explain why you're doing this; that will actually make things even weirder. Instead, keep a printed copy of this column with you at all times and hand it to your ex-seatmate as you depart. Handing out printed copies of websites you enjoy is a totally normal, nonthreatening thing to do.