This is just like the debate over YAML. In both cases, the language is simple enough, and people use it sanely enough in practice that I just don't care about the warts. Contrast this with something like C++, where the warts are less avoidable and therefore more worthy of notice. Markdown as I use it is functional and simple and no one has suggested an alternative I like better, so I keep using it.

Also, as I use it, Markdown is effectively plain text. I very rarely look at "rendered" markdown. I guess in practice I actually use "plain text" that just happens to look a lot like markdown by this article's definitions.