Markdown can certainly seem illogical or intimidating at first glance, especially for novice users which I assume is what you mean by "most users". Markdown looks a lot less techy and ugly compared to HTML (and it's vastly easier to type), so it's a good middle ground when your audience might want some powerful editing abilities.
While Markdown can be very good for somewhat technical users, don't forget that the syntax is completely opaque the first time you use it.
Note the list of notable sites using Markdown Wikipedia provides; many of them also include WYSIWYG editing buttons. A nice thing about Markdown is that unlike HTML it can be included in text with being too confusing.
Stack Exchange is a good example of how Markdown can be presented well to a less-technical audience; those with no concept of markup languages can use the bold and italic buttons to mark up text without ever intentionally typing markdown. Stack Exchange's dual preview/edit panes also allow you to see the raw text and formatting at a glance.
However since the Markdown is presented to the user it can quickly act as a learning tool so frequent observers note "aha, when I make this bold it's just adding two stars on either side of the word!" The power in this is that normal users can use the discoverable, conventional buttons but frequent users can pick up Markdown as they go to make them more productive.