I had this "great" idea of having mines that exctract minerals and factories that make goods in my game.
So you can place a mine on a goldmine and then it'll start extracting the gold resource at a certain rate? Then you have a factory that makes some product that uses gold? I'm assuming this is some kind of RTS?
The thing I would say is that this aspect doesn't really need to be that exciting does it? I mean the end product is what people would be excited about right? For example in Age Of Empires you put workers on a goldmine and forget about them until the mine is used up, but it's the things you can make/buy with that gold that really matters.
However, what you can do is somehow limit how many mines they can have collecting certain resources or something like that. You have to make them make a decision on what resources they need and not let them just be able to collect all resources at all times. Now they have to think about this process. Maybe you do this with some kind of energy source that can run only so many mines or something like that.
Limitations is what makes life & games interesting. If we always got everything we wanted then it becomes boring, but having to work around limitations makes us use our brains more and be creative and make unique decisions. You need to create some kind of limitation around these mines to limit things.