Can an existing furnace flue be used to vent bathroom exhaust fan
I see no problem with using the old furnace flue for the bathroom vent as long as that vent has no other connections such as off to a gas water heater.

The 16' rise of the old furnace flue can represent a challenge for a small bathroom fan to push air through. The column of air presents a back pressure that the fan must overcome in order to be able to produce positive upward flow out of the flue pipe. A small capacity fan may be able to cause air flow to occur but it may be way less that what is needed to adequately vent your bathroom. 

So I would suggest selecting a bathroom fan that has a greater than normal flow capacity than would be needed for your installation under normal circumstances.