I can't speculate on antidaily's reasoning, but I can tell you why I don't like this way of doing markup. (I thought I was the last one.)
First is the lack of standardization. Asterisks traditionally meant boldface, I thought, but in some of these systems they mean italics. Some use underscores for italics, while others use slashes. And those are just the common conventions; the less frequently used ones tend to be even less standardized.
Second is the fact that the more conventions these languages implement, the more likely I am to emit one unintentionally, and then have to figure out how to escape the input so it's treated literally, if the language even supports that. (Note for instance the long-standing Lisp convention of putting asterisks around special variable names.)
Thirdly, the syntax rules of these languages are often ill-specified and incorrectly implemented, making it difficult to tell at times how to get the effect I want.
* Links are backwards (text,link instead of link,text like HTML anchors)
* Link syntax is pretty arbitrary (why braces and brackets?)
* Single line breaks are swallowed unless you append two spaces to the line. (How is this a "natural" formatting?)
* Footnotes with asterisks turn into bullet lists
Most or all of these are resolved by various implementations, but that's just another reason to hate Markdown: the inconsistencies between implementations.
I don't loathe it, but I don't like it, and I'm sad that WYSIWYG text-editing software is still so bad that a kludge like Markdown seems like a good idea to people. Markdown isn't optimized for people (it's harder to read than properly typeset text, and when writing it you pretty quickly have to remember syntax details, like what sort of brackets to use for links), and it's not optimized for computers, either (it's harder to parse than, say, XML).
