WYSIWYG is #1 reason I believe.

Markdown is fundamentally WYSIWYG - you edit something and you get it rendered 1 to 1. Either in plain text (a.k.a. "source") or when it converted to HTML/CSS and then presented.

WYSIWYG requires 1:1 mapping between "source" and "presentation". Markdown is exactly that. While HTML/CSS is 1:N mapping - same presentation can be achieved with many combinations of HTML/CSS rules. That's why "true WYSIWYG" is barely achievable with HTML/CSS.