I picked at what I mean a little in a post this summer: https://t-ravis.com/post/doc/the_gizmos_role_in_markup/
(I've also made the first post in an unfinished series that will continue to explore these ideas about markup, but a bit less directly: https://t-ravis.com/post/doc/what_color_is_your_markup/)
Similarly, for things like comments on message boards or blogs, a user can just dump a bunch of text into the text box without knowing the first thing about Markdown and expect it to look more or less like how it was entered, with paragraph breaks and such. If you force these people to use HTML instead, you're forcing them to at least learn and use <p></p> - which is probably simple for those of us reading HN, but I don't consider it a reasonable request for the normies on Reddit.
So, sure, HTML is quite good at what it was invented for, but not everything that involves text input on the internet or elsewhere should be HTML.
For me, I use Markdown because I can transform it with Pandoc and my own filters to any other kind of document: