Because web browsers are supposed to render HTML, not markdown.

When presented with a file full of markdown, how should the browser present it? As a webpage? PDF? Plain text? Something else?

Once that format is chosen, markdown doesn't have any way to control that presentation. Black text on white? Opposite? Something else? How wide should paragraphs be? Each author and page has different preferences and requirements.

That's not considering the dozens of flavors of markdown, each with their own extensions, features, and subtle edge cases. See XKCD on standards: https://xkcd.com/927/

20 years ago, people were trying to make web pages out of XML. It didn't catch on. Markdown, likewise, has some pretty obvious pitfalls and feature deficiencies compared to HTML.