I use a water filter, too. After researching them, I found what they filter out depends on the size of particles the filter material allows through. (That's why there's different filters for lead.)
Anyway, even if your filter does take out flouride, you should be ok if you brush twice daily - according to my dentist...
He feels that it's not so much a problem getting enough flouride (because we only need trace amounts), but more that people don't floss as well/often as they should, and the plaque doesn't allow the flouride to get to the teeth as well...
(I'm not a dentist, though...) DRR