I asked this question ages ago and it was pointed out that "sub" isn't a reddit specific term. It's been short for "subforum" since the first BBSes, so it's basically a ubiquitous internet term.

"Sub" works because everybody already knows what you mean and it's the word you intuitively reach for.

You can call them "communities" if you want, but it's longer and can't easily be shortened.

I just call them subs now.