Both Wordpress and Gmail have full blown wysiwyg, and many other sites such as facebook and Twitter have wysiwyg-like features in their messaging/commenting. What site bigger than these use markdown?
User tagging. It's not a traditional WYSIWYG editor feature, but it means the implementation of the actual editor input field faces the same problems WYSIWYG editors do.
> Yeah, you see plain text, and you get plain text. Big deal.
Nope, not quite. @Tagging someone will suggest and highlight users. Not a full blown WYSIWYG but in the same calibre of technical problems and reasons why people stay away from WYSIWYG.
Wordpress WYSIWYG (TinyMCE) is notorious for bugs - I experienced them first hand - and it's not a website, it's a software people install. Big difference.
I had forgotten about Gmail, so I guess this is the exception to the rules. On the other hand, markdown is supported on Reddit, Stack Overflow, Github, and many more.
Stack Overflow and Github's primary audience is developers. Reddit's started out with a mostly developer audience and still today has a huge crossover. It absolutely makes sense to support mark down if your audience is developers.
I don't find gmail to be an exception to the rule at all - all the big webmail providers offer full WYSIWYG support.