Depends on where you get your water as to how bad it is, but there can be all sorts of nasty critters in surface water. My grandmother had amebas for a while in the 40s or 50s and it caused her some serious problems.
While a stream close to a spring head may look okay, you might not realize a dead animal upstream that could cause serious problems. Also streams can go back underground, so what you think might be clean spring water, might have actually been running on the surface.
The idea is to filter out all the big stuff, IE amebas, protazoa, parasitic worm eggs, Giardia and other nasty cysts etc, and use chlorine to kill the viruses and bacteria.
I use MSR drops and have not had any problems. I give it 10 minutes.
If I am not wrong Iodine, pretty much kills it all.
Probably the most foolproof is boiling water.