It's a different markup. One that many people find easier and more natural to write. Of course, different people have different opinions on that.
For people who find writing and reading markdown nicer than HTML it makes sense to use markdown as the base format that you write everything in, and then convert to different formats as needed (html, pdf, whatever).
For you, HTML may play that role. Personally I find HTML ugly to read and write.
To summarize: markup is better to read+write. But the difference is almost zero. Anything other than trivial markup is a mess; exceptional layout often impossible (and I value the ability to creatively use layout to get my point across). It doesn't support wysiwym editing (very well). It isn't trivially statically hostable - and if you try it's fragile and flashes uglily. Many flavors exist that are slightly different.
I prefer flexibility, consistency and simplicity over micro-optimizing source readability.
I also like the idea that the "source" is right there on the page rather than a separate "API" - the dream of XHTML+XSLT. When I originally set it up I wanted the page to be readable using Telnet - which I think it is, more so than one rendered on the server would be. I couldn't tell you now why that seemed important though.