See, deep down, this is what bothers me about it. They haven't even added a decent questing system but modders have, and Notch gets the cash while articles like this prevent anyone from really making any money at it.

I don't know if that is the only reason. I mean Quake had quite a good set of mods pretty much written in C++ type of code. More recently you can find modded server for games using Python or LUA for their game logic, official or not.