I think this is a bit short sighted. I like Markdown and I'll eventually integrate it into my product, but to discredit the usefulness of WYSIWYG would be foolish. Maybe there is a lack of good implementations for it to show any value. I'm currently evaluating redactor (http://imperavi.com/redactor/) as my WYSIWYG editor and I've been happy with it so far.
For example this is how I render the html that is generated by redactor:
http://screenshots.gitsense.com/wysiwyg-1.html
If you click the edit button on the bottom right hand corner, it'll bring up the WYSIWYG editor:
http://screenshots.gitsense.com/wysiwyg-2.html
And if I need to do a complex layout like the one in the screen shot, redactor lets you edit in raw html, as shown below:
http://screenshots.gitsense.com/wysiwyg-3.html
If you are working on a product and believe Markdown is the only way to go, you'll probably do yourself and your customers a disservice.