As in the rural parts of the U.S., when you get out of the cities, there are a variety of systems for collecting water, from municipal systems to wells to run-off collecting and even pipes into streams. For the most part, I find the water quality in Chile to be excellent. In the mountains, I often drink directly from the streams.
Using common-sense is advised. If you see that the pipe is being fed by a stream with a cow standing in it, well, you might not want to drink that water. I know some of my guests have more sensitive systems and get very mildly irritated – just like they can when they visit Colorado. My advice is try the water for a day or two, if your system changes, and you become uncomfortable, try bottled water and see if it improves.