My take on it is, three days without water (less if it's hot or you're physically active) and you'll be in real trouble, so I'd definitely drink when I felt I needed it.
I'd think the majority of 'bugs' in remote water sources will take longer than three days before they have any drastic affect on you. (giardia takes 1-2 weeks before symptoms show, average about 1 week after infection) Better to get out with the trots than not get out at all!
It can be a mistake to drink from flowing or turbulent water, if there is a still 'side pool' of water at the edge of a creek or river, then take your water from that and always take it from near the surface.
The reason being, cysts like giardia settle to the bottom in still water - if present, they will be suspended throughout turbulent water. Also, I've heard that the sun is a powerful disinfectant, so strong sun rays may well have a beneficial affect on still surface water layers.
It may not always be possible to boil water for a variety of reasons, so I reckon it's a good idea to always carry a small bottle of purification tabs on your person or in your kit, just in case....