I stick it in my deck fill for the holding tank to flush it and assume most others do the same. I find another hose to fill fresh water with.

If there is a hose without a pump out (like at a fuel dock) I'll use it. We have a .2 micron filter (not 2 micron) in the galley for drinking water and use bleach in the main tanks. That's all we've ever done and have never been ill. It doesn't make sense to filter the water coming in as we use the boat itself to collect rain water.