This is called the "bus rule" around here, you don't sit beside someone if there's a still a set of seats you can have to yourself.

I'd be more worried if they did sit beside you, as that'd be considered a bit creepy.

Are there other empty groups of seats? I find people generally spread out to avoid others.

It's certainly something I do. I'll sit next to someone (choosing the least talkative looking people first) only if there is no other choice.

Do you sit near others, even within a few seats, or generally as separate as possible? Most people in my experience sit away from others. If I see someone sitting near/engaging with strangers I generally assume some mixture of mental illness or ill intentions/scammy behavior.

People leave a space between them and someone else to have some personal space and respect other’s personal space

I do not think it is you at all. I am on the autism spectrum myself and I purposely sit away from others because being boxed in by other people causes me to be way overstimulated. I don't believe it is intended to be a slight against you, rather it's just people's preferences.

That's kinda normal in my experience. People leave 1-3 seats between each other if the train is empty.

Are you heavy? That can be a reason, as bigger people simply take up more seating space.

Any face tattoos?

Happens the same to me. I learned to give a single f. I even find it a bliss, some people smell bad, are with the headphones killing their eardrums, pushing me because their are too big, farting, whatever… is not a pleasant experience one would want to do on purpose.

I prefer to sit alone if possible

Do you play loud music?