I agree that giving out free cups of water doesn't seem to make financial sense. Even if you have to go to the window to ask for it, it still doesn't seem to make financial sense.
However, I assume Disney gives out free water because Disney sees some benefit to it, even if it's not immediately obvious.
Good will, of course. And that is important to Disney, even though it doesn't always seem that way.
But I also think that keeping people healthy and hydrated is a good thing for Disney.
Being dehydrated makes people tired and grumpy. Tired, grumpy people probably don't spend as much. They probably don't make as many "happy memories", either.
Tired, grumpy children tend to cry and act out a lot, which impacts the enjoyment of others. Even grumpy adults can make the people around them, guests and cast members, miserable, too.
Finally, consider how many people visit Disney World every year. Most of those people come from places with cooler, less humid and sunny climates. They are not used to drinking enough water for spending a day walking around in Disney World.
We are probably talking about hundreds of thousands, possibly millions of guests annually that are borderline dehydrated. Most of them will be fine: just tired and grumpy. But some, especially the very young, elderly and infirm, may not be fine. Not really. Dehydration increases the risk of a lot of serious medical problems. Out of millions of visitors, some may well experience something very serious, even fatal, that could have been avoided if they had just drank more water.
Disney doesn't want their guests to get sick. Medical emergencies in the parks are bad show. Disney goes to great lengths to avoid them. Free water is pretty cheap insurance against dehydration related medical emergencies.
And, in my experience, Disney employees are all very kind and compassionate people. Even if there wasn't any financial benefit, I'm sure every Cast Member I've personally ever met would like park guests to stay hydrated and healthy, because they sincerely care about them.
Giving out free water and making it as easy as possible for guests to get it, is something nearly every individual Cast Member would personally agree with, even if it didn't make financial sense for Disney (but it probably does.)