It feels like there's a certain number (maybe Dunbar's like you said) at which people stop seeing a community as a group of disparate individuals and start seeing it as some sort of a collective hivemind.
You see this regularly with comments like "HN/subreddit/etc is so hypocritical. One day they're in favor of X, the next day they're against it", in which the poster seems to fail to realize that in a community of tens of thousands of people, chances are it's entirely disjoint subsets of the group taking those positions.
I don't see that kind of thing as often in smaller message boards. When you recognize everybody's name (or at least their avatar), it's a lot clearer that it's just Bob and Alice who support X and Eve and Mallory who don't.
It seems natural that such a failure to see the individuals that make up a group would lead to a decline in civility.