- Have you ever tried using git on a docx file? The best you have is file history, but good luck trying to merge branches, create/apply patches, cherry-pick commits, rebase, or view line-by-line history.
- You lose the interoperability of plaintext. Any editor can open a plaintext file, and consuming a plaintext file is straightforward. Not so with binary.
- You lose a lot of choice about how you want to interact with the file. Syntax highlighting, TextMate bundles/snippets, and hundreds of editors and plugins are available to both create and consume Markdown (and many other text formats).
I agree that rich text editing is great, but may I suggest looking into another plaintext format besides Markdown if you can't find a wysiwyg markdown editor you like? There's RTF, TeX, and others -- each with a great ecosystem of tools around it.
More generally, if a particular plaintext format doesn't meet your needs, I'd argue the problem isn't necessarily that the format is plaintext as opposed to binary. Binary can be nice for serializing C/C++/etc. objects and for packaging resources, but there are tradeoffs.