When I installed ceiling fans many years ago, I wired separate switches for the fan and lights. Instead of using one run of 14/3, I used two runs of 14/2 NM-B cable.
At the switch, a single supply from the panel enters and the hot is pig-tailed to both switches, the neutral is wire nutted to the outbound neutrals, and the grounds are pig-tailed to both switches and the outbound grounds. The hots from each cable are connected to the other screw on each switch.
In the ceiling, the neutrals are wired together and to the single neutral from the fan/light combo, the hots are connected to the appropriate light or fan hot, and the grounds are all connected.
Please see this fine piece of artwork depicting the wiring. Note that the red circles indicate wire nuts (of the appropriate size for the size & quantity of wiring), and that the yellow cable doesn't necessarily indicate #12 wiring (some were #12, some were #14), but all are on 15A breakers:
Note: I believe that there is only 1 neutral connection at the ceiling just like the ground, shared by both fan and light wiring. However, I'm not going to update the drawing since I did it in MS Paint and it's a royal pain to make changes. I might be persuaded if there is a great outcry.
Is the neutral is considered paralleled (if so, is that a problem) and did this wiring situation meet code when it was installed in the early 1990s? My state is currently on NEC 2008 (with few to no modifications, as far as I can tell), does it meet current code?