[yojex]

So this might seem weird, but there are many people who do not at all feel that way. I can't even begin to imagine what feels condescending about someone using "so" as a filler word.

For people with a bit of social anxiety, it can serve as an easy and comfortable lead-in to share a thought when they can't think of a better way.

[malvosenior]

I think if you read your reply with and without the “so”, you’ll see what I mean.

Your second paragraph is probably one of the reasons people do it but it’s also the reason it come off passive aggressive, which when disagreeing with someone sounds condescending.

[yojex]

I included it in my reply to see what you thought of it :)

I hadn't considered it in the context of disagreement; I think I can see how that could rub people the wrong way.