At the end of the day, there’s limited space onboard and we can’t have endless supplies of 500ml bottles for everyone. There does become a point that, on full flights, we may have to start refilling from a big bottle. It’s literally the same water - Highland Spring 1.5L vs. Highland Spring 500 ml (or Crystal Geyser), but you’ll be surprised how many people are bothered by this.
I recognise the germ argument, but at the end of the day if germs are something you’re truly concerned about then an aircraft isn’t the place for you.