Unless the pain is due to repetitive stress, which tends to be my problem. I can easily do heavy squats, but riding a bike for 30 minutes kills my knees.
You might want to talk to people at a bike shop. When a bike fits you and is adjusted properly, pedaling should be very gentle on your knees. You might have your seat at a bad height, point your toes in or out while pedaling (twisting your knees), etc. If you're using clipless pedals, they'll probably need to have their float adjusted.
(If you're riding a fixed-gear bike with no brakes and slow down by backpedaling / skidding, that's another issue entirely. Just get a front brake.)
This could be an issue of pedaling too hard. I started cycling, and when I first started, I was pedaling at a low cadence (pedal rotations/minute, I was probably at < 60, I didnt have a bike computer then) and would get knee pain on shorter rides (~5 miles). Now I ride between 80-115 cadence on rides over 20 miles and experience no pain. The other problem is that the bike wasn't properly fitted for you.
It is just the other way around for me. I ride in a fairly high gear with low cadence, and get a muscular burn in my thighs, because when I try to push a higher cadence in easier gears my knees start hurting.
FWIW, I had the same problem until I realized one thing - I like laying down on my stomach with laptop in front of me, knees firmly pressing into the sofa. As it seems now this caused prolonged dislocation of kneecaps which caused problems later when biking or doing similar cardio. Two weeks after I stopped doing that the bike problem went away.
I've had issues with knee pain my whole life - at first it was because of "growing pains".
Any high rep stuff to muscle fatigue I've tried causes pain for several days. But strength training helps it in general and makes it a non-issue in day to day life.
You may have an issue similar to mine. As the result of several minor injuries in my late teens I had many joints x-rayed at different times over a few years, and every doctor commented that my joints were odd, at one point the doctor had my other wrist x-rayed so he could compare it to the injured one. The bones in my joints are further apart than is normal. This results in a greater risk of injury to some joints, so one of my main reasons for weight lifting is specifically to strengthen the muscles that stabilize the joints.
I also have a bad knee, I guess from repeatedly hitting the ground with it while playing handball when I was young(<20). It started to be really painful in long car rides, whenever I standed up for long times or had long walks but it never bothered me when I had played some sport.
A year ago I got into a gym and I feared that my knee would break down, amazingly I learnt what you refer to, that weight lifting is one of the best ways to strengthen muscles that are important to the joints. When I thought of weight lifting I just thought of stressing the body, my idea now is completely different, weight lifting is a way of activating some of your more obscure muscles. Never again I got any complain from that knee.
