You see I have always viewed the opposite as being unfortunate and unfriendly. I have seen the efforts made not to sit by people as offensive. Maybe this comes from having grown up feeling no one wanted to sit by me. I took people taking seats away from me as appallingly mean - there must be something wrong with me that they don't want to sit beside me. So I guess that is why I make a point of sitting next to people on public transit. I do so not to make them uncomfortable but rather the opposite. It is my way of indicating I accept them. A shame to learn this kind effort is backfiring.
I ask those of you of the mindset this is rude to consider the possible true intent of the next person who sits down beside you. Are they trying to be actually nice and observe some social etiquette perhaps?