I was planning on making a cake and covering it in fondant. However it just dawned on me that the filling I was planning to use needs to be refrigerated. I'm thinking I can't cover the cake in fondant and put it in the fridge. That would ruin the fondant...right?

It shouldn't

It won't ruin the fondant. What happens is that once you take the cake out of the fridge, condensation will appear... you know, water and fondant are not good friends. Try some filling that you can keep at room temperature. Good luck!

Lightly cover the fondant with plastic wrap when you put it in the fridge. It helps keep the moisture away.