$2.25 is a little silly. Water should never cost the same as soda. Maybe they wouldn't be so much if they didn't give so many away to sleeping car passengers. I never drink it anyways and always bring it to the SSL for someone who wants it to have it for free.
When I review the prices, even low bucket prices, for sleeping car tickets - I don't see anything being given away for free.
That said, I agree the cost of those small bottles in cafe cars does seem a bit much. It in general strikes me as strange that sometimes, bottled water costs more than gasoline - and not only on trains.
But it demonstrates that often the cost of products is not so much in the production of them, but rather in the packaging and handling and shipping and storage.