However, as Markdown is supposed to be nothing more than a superset of HTML, you can simply reach for CSS. It won't always render the best if you're moving from Markdown to physical medium, but that's largely dependent on the engine.
If this is an input to a website, for example, the webmaster really doesn't desire everyone to be able to reinvent the blink tag, or be able to express everything in rainbow fonts.
In which case Markdown shines, for it's ability to express simple markup, that can be safely expressed.
Not at all.
PS: By the way, you are currently commenting in text without colors - how do you feel?
You (and other posters) can ironize as much as they want, the truth is dealing with colored text in Markdown is equals to inputting raw HTML, as which point mixing the two markup languages is more painful than going raw HTML.