To use Ubuntu to upload FitBit data you need libfitbit which is available as ppa now. However I couldn't find configuration instructions. I also wonder if cuttlefish could help to get the same functionality as on OS/X: stick the stick in and get the upload going?
So I haven't actually been able to set up the fitbit using libfitbit, I had to use my roomates Mac to do the initial setup.
As for the "sticking in the stick and get the upload going", I included some udev rules in that package (I believe the original author wrote them), and it should just work when the fitbit is plugged in (once the initial setup has been done).
If it doesn't work, you just need to plug in, and run