Part of it is educational. And I don't mean that in the "you only have a 9th-grade education", sense. Every online community has unwritten safety rails established by the member community, and people who are new, or don't feel like those boundaries should apply to them will cross the barrier into oncoming traffic either by accident or on purpose to see who swerves. Until they're corrected and figure out the system, they can cause problems. They need to learn what is, and what is not OK. This is what the report system is for, and what the community leaders try to do.
Another part of the educational thing is that this site is full of very knowledgeable folks who take VERY clinical, no-nonsense approaches to solving problems. Short, direct questions and answers, quick responses to things that are silly/wrong/troll-y, that sort of thing. They're golden-hearted people, but they're focused on solving the problem quickly (because a lot of times it could be a life or death situation and time is critical). That can and very often does come across as rude, mean, etc. We all have a very particular tone in our writing style. Those range from very cordial, to "dude may be a serial killer". Everyone's busy, and it leads to toes getting stepped on and feelings hurt inadvertently. You have to look at the response as objectively as possible and not immediately react emotionally, because 9/10 times the person is genuinely trying to help and not really being a jerk. You have to know the people involved and understand them a bit, and that only comes with time.
For the rest, well, the anonymity of the internet is a blessing and a curse. People are far more inclined to troll when the repercussions for doing so are basically nonexistent. That isn't a dig at the site admins, but in a real sense, the worst that can happen to a member here is a site ban in
most cases. Your neighbor isn't showing up at your door to yell at you about some insensitive comment you made on a chicken forum, and your boss isn't going to write you up for it either. The true behaviors of people come out when they feel like there's no social penalty for being themselves. It's a problem in all online communities, and there's a very real up-welling of intolerance and stupid behavior in society as a whole. BYC is simply a microcosm of that reality. People in general are far more cynical and intolerant today. The only way to solve that is to get enough humans to start being humans again in order to divert the toxicity. The internet is a wild and dangerous place, and always has been. There are some deep-rooted sociopolitical reasons for that, but it's well beyond the scope of this conversation and well outside the safety barriers for BYC I mentioned above so we're not gonna go there.
As far as side conversations in threads, well,

. There is not a snowball's chance at Kilauea of that changing.