Fit is one important aspect, but only one.

There are all kinds of reason for general knee pain, general posture, systemic condition like OA or RA, poor skin condition, weakness, neurological conditions, mal alignment of the hip, biomechanical adjustment due to other sports/work nature, amunst many other factors. Even Sexually Transmitted
diseases can cause knee pain.

The "correct" treatment might be to strengthen the glutes roles in maintaining rotational stability of the femur, or encouraging the glide of the knee cap to track better. More information is required as to the nature,location of the condition to rule anything in or out. See a physiotherapist and get a differential diagnosis.

And yes, also make sure your "fit" is optimal.

This is 2010, can some road cyclists realise than "fit" is not the only answer to knee pain!