I have heard different things about that - I don't know if they really do get it for free, or a reduced rate, etc. My husband used to work in the restaurant business and said the soda cost them pennies then. I can't imagine it's a lot more pennies now. And with the mugs, they aren't using up paper cups - just ice and soda.
Even if it cost Disney .10 per fill-up, it would take maybe 120 fill-ups to start costing Disney money (if the mug cost $1.00 or so, which I'm not sure if it'd cost that much for them). And in that time, there is probably quite a bit of food being sold as well.