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Markdown is useful: an easy-to-use notation system that allows you to mark up your text in a safe, fast way.
Because you're never letting your users write raw code, there aren't any worries about them posting malware or exploit attempts, or accidentally writing bad markup. At the same time, simple lines and dashes are converted to valid HTML. Everybody wins.
But when you're writing your own site, you don't need to worry about those things. You don't care about you posting malware or exploit attempts. (Either you want to, or you won't.) You also don't need to worry as much about bad markup - and if you're not proficient in HTML, you can install a WYSIWYG editor, like the one in WordPress. Unless you're a Dr Jeckyll who morphs into an id-like alter ego without warning, you don't need to worry about your own trustworthiness as a user of your own system.
On a self-hosted #indieweb site, all #markdown does is restrict what you can do. It has a syntax to learn, just like basic HTML does, and because you actually have to keep in mind which HTML tags it uses when you write it, it's actually a little bit more complicated to remember.
I like a lot of the goals of new publishing platforms like Ghost (I backed it on Kickstarter) but this feature sticks out like a sore thumb to me. I'm not at all sure this is the best writing experience on the web. And I don't see what's wrong with HTML.
Updated to add: I've had lots of feedback by people who point out that they just want to write text, not HTML, which is more than fair enough. But surely this shows demand for a smarter, context-sensitive rich text editor rather than another syntax to learn. Why couldn't an editor know to start creating bullet points when you type an asterisk and a space at the beginning of a new line?