Three things can help:
1. It has become "stylish" to sell bikes with absurd gearing (four or five speeds between 90 inches and 130 inches). Your knees would prefer that you stay in gears between around 55 inches and 75 inches, and get your speed by building up your cadence rate to 90 RPM's or 100 RPM's.
2. It has become stylish to "lock" your shoes to the pedal, ensuring the precise same angle of stress on your knee throughout a ride. Instead, use shoes and pedals that make it easy to shift your foot during a ride, moving it half an inch forward, and half an inch back, giving different parts of your feet, legs and knees a rest.
3. Play with the height of your saddle. Most formulas for saddle height assume you are a young guy who races bikes. Those formulas have the knee and leg almost straight when the pedal is at 6 0'clock. Most people don't race for a living. Dropping the saddle an inch or so below the "Pro" level provides a more distinct knee bend with the foot at the bottom of the stroke. This height provides less stress to the knees and to the crotch area as well.
Start out your rides slowly. Take it very easy for the first ten or fifteen minutes of riding to give your legs time to loosen up and warm up.
Try to ride everyday. Guys who ride hard once or twice a week seem to have more pain than guys who ride everyday.