What you're seeing are actually probably fungus gnats... they're about the same size as fruit flies. The flies themselves aren't that big a problem... but if there are enough of them, the larvae that live in the medium can cause root damage.
However, if you have fungus gnats, this probably means that you're over-watering, which is a bigger problem than the gnats
This would be a good time to evaluate your watering practices and cut back a bit so that your media dries out (or at least ALMOST dries out) between waterings.
- Matt