To take one of the more innocuous examples from the past consider the Red Scares. It was fundamentally driven by people believing that they have the moral high ground against a certain view. Communism is bad and therefore it was okay to do bad things to people who held positive views of such. And it was simply 'common sense' that supporting communism in any way, shape, or form was an absolutely abhorrent thing to do. And I use that as an example only to avoid any rousing of emotion but the exact same logic drove the KKK, Nazis, and nearly every group, sinner and saint alike, throughout time. Moral authoritarianism is again, a very dangerous thing.
And I certainly do not agree with you on this was or will be the way of society. Words and actions are distinct. I think an ideal society would have no tolerance for intolerant actions but an unlimited tolerance of words. Indeed this is even what the actual quote, often egregiously bastardized and misused by the most intolerant of today's society, on the 'paradox of tolerance' fundamentally suggests. Even looking back now at the Red Scare we can generally see how quaint our intolerance was. There's no need to name and shame communists - the view itself is simply not supported by enough of society to matter. And if it does become supported by enough of society? Then we try it, almost certainly fail, and continue on our disjointed path "forwards" as always.
I think you've hit the nail on the head here.
As Scott points out in https://slatestarcodex.com/2019/04/02/social-censorship-the-... censorship is mostly used against groups we think are dangerous (mostly because they actually have a fairly large amount of support). Someone advocating that going to church should be mandatory and divorce and blasphemy should be illegal will get eye rolls, not anger.