In Denmark I rarely, if ever, see water fountains. If I saw one, I would never drink from it. For me, personally, it's a sanitary issue. There also seems to be studies that link them with pathogens and bacteria, wikipedia links to some[0].
If you chase that link down, you find it is referring to the presence of pathogens on the handles of toilets, the surfaces of water fountains, and other moist surfaces like water play tables, in child day care centers. This is not the same thing as transmission through the stream of water itself.
My take away from that is to be careful of touching such surfaces, but not to worry about the stream of water.
[0] https://en.wikipedia.org/wiki/Drinking_fountain#Cleanliness