Is the pain right below your knee cap on the the patellar tendon itself? Do you have pain during any other activities or just cycling? Are you stretching your quads, hamstrings, calves, and IT band every ride? Deciding whether your kneecap is tracking wrong.(i.e tight muscles or a muscle imbalance) or whether its a tendon is sometimes hard to determine. If you can pinpoint the pain its probably a tendon problem but if the pain is more widespread around the knee its more likely your patella is tracking wrong.
Make sure your seated correctly and that your cadence is at least 85-90 rpm. If you cannot hold that cadence up a hill stand because it is easier on your knees. If your leg muscles are tight that might be your problem and stretch but do not overdo it. There are knee straps/braces that are made for tendonitis that could be beneficial. Try waiting a little while before you ride again to rest your knees and if the pain persists you need to go to a pysical therapist who specializes in sports medicine before it gets worse.
Right now I have been off the bike for 5 months because of knee problems and hopefully it will get better soon. You can read my post about all the problems I've gone through.
http://cyclingforums.com/t278027-17-year-old-with-major-knee-problems-help.html If you have a knee problem catch it early and get advice from a professional. Do not ride through the pain!