What strength program do you recommend for bicycling?

What is the best way to strengthen the hips other than squats since my ankles and low back lack the ROM necessary to do squats correctly?

Actually, a great program for a cyclist would be any of the the Get Lean Programs. These programs focus on muscular endurance with just enough work on muscle strength and power to improve your cycling performance without getting too massive which would hamper your cardiovascular performance capabilities.

If you can't squat with free weights, you should try either the Smith Machine squats or simply do the Leg Press machine. These 2 exercises are much easier to perform, technically speaking, but will still give you adequate levels of stimulation to develop hip and leg strength.