Yes, however part of it is technique: Flossing will probably always hurt if you are just sawing into your gums with string all the time. The idea is to use it to clear stuff off your teeth, so try to get the floss to conform to the curves of your teeth as best you can. If you're using flossers, consider switching to regular string. They also sell flossing toothbrushes.
However you floss, try to keep it up along with regular brushing using fluoride toothpaste before bed. I brush when I wake up too.