The first thing I do when I work in an editor with a mini-map is -- turn it off. I find it mostly the most useless feature for coding, and for sites it seems to be equally useless. Why? 1. Stuff is too small to really make out where I'm going or navigating. 2. Short or long pages, both don't really benefit from the loss of screen real-estate. Or the distraction really. 3. Other tools like a proper index with descript…
I would find this very useful on a site like Wikipedia where I often know the section I want to jump to before landing on the page. (e.g. I want to see the number of goals Messi has scored each season at Barcelona and I know there's always a table at the bottom of most wiki articles regarding historical stats for soccer-players). I could see from the mini-map where the tables are jump straight to it.
Like you said, the the text is too small to make out where you're going or navigating. But most often I find myself visiting sites that I've visited in the past and for those I have a good mental image of what the page already looks like. I can use the hints from a minimap to jump to the relevant section of the page.