Well, I think Dwarf Fortress could provide some basic education about :
- Ecology / meteorology : The world generator create forests, lakes, rivers and deserts based upon things like precipitation, cloud shadow or eroding. The whole process is coherent and based on real-world data.
- Geology : The different kind of stones in DF are based on real-world stones and ore (not taking into account the adamantine, of course), and the system of layers is also quite realistic.
- Economy : Job management, input / output of resources, external trade, wages, a pretty good recreation of some industries (weaponry, food, and some others)... avoiding unemployment is a pretty complex task in dwarf fortress, for instance.
- Politics : There's some notion of social classes (skilled dwarves vs unskilled ones), and the noble thing. You also have to satisfy the population if you want to avoid troubles (even if it's less violent and more self-destructive that the human counterpart).
- Architecture and room design : It's not that easy to figure out how to optimize commute time, or the design of the public dining rooms or corridors to avoid crowding, etc.
- Also, tactics : Even if it's going to be totally revamped by the next update (but then it'll be better probably), you currently have to prepare carefully for each battle, by choosing the right spot for each unit, escape routes, elevation, ammunition...
- ...
There's probably more thing that you can learn or practice by playing DF, but these are some that spring to mind.