Even if the syrup is free there are still other expenses I am sure that are not covered.
Such as the cost to carbonate the syrup ,the cost of the dispensers. the cost of the ice, the cost to deliver the syrup, the pay for the CM's setting up the machines, the electricity to run the machines, the cost to maintain the dispensers, not to mention the cost of liability insurance in case of a lawsuit from a "slip and fall".
I am sure there other expenses I am missing but I assure you there are a lot of "hidden costs" in that mug of soda and even pennies tend to add up when hundreds of thousands of mugs of soda are dispensed weekly.
JMHO
How long does it take for the pennies to add up to $12.49? Liability insurance? Either the resort has it or it doesn't. They don't buy insurance on a cup by cup basis, or even product by product.
Of course there are expenses with dispensing beverages, and if Disney was losing money hand over fist those machines would have been ripped out long ago. But like I said before I do think Disney does need to either enforce their written policy or change their written policy to match their common practice.