No problem at all.

Power at the switch

If the power feeds into the switch box, you'll simply pigtail the ungrounded "hot" conductor to feed each switch. Then you'll run 14/3 or 12/3 nonmetallic sheathed cable (Type NM); whichever is appropriate, between the switch box and the ceiling outlet. Then connect the white (grounded "neutral") from the feed, to the white (grounded "neutral") to the ceiling box. Connect all the bare/green grounding conductors, and don't forget to ground each switch and the box if it's metal. Connect the black wire from the cable that runs to the ceiling, to one switch, and the red to the other switch.

When you wire up the fan/light. Connect all the grounded "neutral" conductors together. Connect all the bare/green grounding conductors together, and don't forget to attach a lead to the box if it's metal. Then connect one ungrounded conductor to the light, and the other to the fan.

Power at the light

The old way

If the power is at the light, things are slightly more complected. But it's still quite easy. Again you'll need 14/3 or 12/3 cable between the switch and ceiling. You'll still connect all the green/bare conductors together at each place, not forgetting to connect all devices and metal boxes. In the ceiling, connect the white (grounded "neutral") to the white wire from the light and fan. Put a piece of black tape around the white wire from the cable between the boxes, and attach the wire to the ungrounded conductor of the fan or light. Connect the red (ungrounded "hot") conductor from the cable between the boxes, to the ungrounded conductor of the light of fan.

In the switch box, connect the red wire to one of the terminals on one of the switches. Put a black piece of tape on the white wire, and attach it to the other switch. Splice the black wire, and attach a lead to each of the switches.

The new way

If your area has adopted National Electrical Code 2011, you'll be required to have a grounded "neutral" conductor at the switch box. To accomplish this, you'll have to run a 14/4 or 12/4 NM cable between the boxes. Then in the ceiling box, you'll connect all the grounds as before. Connect the white (grounded "neutral") conductor from the light, fan, feeder, and cable between the boxes together. Connect the red wire from the cable between the boxes, to the ungrounded "hot" conductor of the fan or light. Connect the blue wire from the cable between the boxes, to the ungrounded "hot" conductor of the light or fan. Connect the black (ungrounded "hot") conductor from the feeder, to the black wire in the cable between the boxes.

In the switch box, cap the white wire (unless one or both of the switches requires a grounded "neutral" connection). Connect the blue wire to one switch, and the red to the other. Splice the black wire, and connect a lead to each switch.

I'm just thinking out loud here. It is hard to state anything with certainty in a situation like this where there is no guarantee of what somebody else did with the wiring a long time ago...so forgive me if this suggestion isn't even worth what you paid for it. ;)

From what you have said here, it sounds to me like that red wire makes its way back to the lights, and acts as the "hot" for the lights. Who knows where the lights are getting their neutral side connection. Doesn't really matter. Obviously it is getting there somehow.

So to make the lights light, your existing switch is getting "hot" from one of the two black wires, and is supplying that to the red wire.

So think of your red wire as the "hot out", and ONE OF the two black wires is your "hot in".

So you need to use a meter to see which one of the two black wires is your "hot in", and treat it that way and cap off the other black. Then use your red wire as the "hot out".

Again, this is just me thinking out loud about what I would try. I take no responsibility for any bad stuff that might result from it. All possible disclaimers apply. ;)