Many people throw coins into fountains and make a wish, believing that this simple action will make their wish come true. There is no realistic or scientific basis for believing this to be true. Instead, money thrown into fountains is left until it is collected by the government or thieves passing by.
Throwing money into a fountain is a waste of money. I do not know what happens to the money that is in a fountain. Fountains I have seen are not protected and the contents available to anyone within reach. If a fountain advertised that the money in it went to a charity or for a good cause, I would be more likely to say that the money would not be wasteful.
Nearly every fountain around the world in which people throw coins is affiliated with some sort of charitable organization. Tossing coins into a fountain is an act of giving, and people tossing their coins should reasonably expect that their money will go to a good cause. Stealing from these fountains is stealing from the needy.
It's not like people are throwing a lot of money into fountains, that would just be silly. But if someone wants to say a prayer, or wish for something good, a small denomination coin is a good way to at least feel emotionally better, especially in particularly bad situations where people feel they have no control.