Author here. I think, for one, Markdown's focus is on writing for the web, and there rich text wasn't good in 2004 (where copying/pasting from say Word into WordPress was always hit and miss, and rich web editors were far less advanced than the Webflow's of today), and was inspired by email where plain text stayed the standard longer than elsewhere (especially on Apple products, where into the late '90's the main Mac mail app and the NeXT email app that turned into today's Mail.app both were plain text editors for sending email).

It would be interesting, though, if Tim Berners-Lee's original dream of dream of the web being somewhere everyone edited had come true, then if better quality rich text editing for the web would have shown up sooner.