They do indeed get regularly flushed through (the aircraft potable water system) with a cleaner and the filters changed. However does this mean the tanks are clean? Or just sterilised? If you ever get the chance, do have a look inside an aircraft's water tank.
It's often been said to me, all those holiday makers, they get to their destination and after a day or two they get the runs, thinking it's the food....most likely the water they drunk on the flight!