Here is a quick numbers check
A 5 Gal box of syrup costs roughly $65 - that makes 320 12-oz drinks.
That is .203 dollars per serving. Adding a couple cents for water and carbonation and you have a soda costing around 22 cents per 12 ounce serving.
That means it will take around 70+ refills to get your value out of a resort mug. More if you add ice.
No, Disney is NOT losing money on soda. I am sure they have a much better procurement price on the syrup and CO2. This will just ding their sale of resort mugs.
I am seeing a lot of short-sighted profit margin initiatives coming up at WDW that, I believe, will ultimately backfire (Monorail service cutbacks, anyone?).