Not sure you entirely right about starting young but would definitely say some peoples knees won't suit anything other than toe clips and even they they may be to constraining. I have had anterior cruciate ligament rebuilt about 12 years ago and continued playing rugby. Got septic arthritis in same knee 3 years ago. X-rays do not show any gap in between joint ie no cartilage left. Had to buy an exercise bike before I could actually cycle on the road again. The advantage of a machine is that you can set the resistance and not the actual terrain. Cycling is zero impact therefore very little pain. I actually get more pain when I have been sitting on bar stool than when I have been cycling.
I am with Acesand8s try clips first still not right go for floats (I assume that means using nothing?) And as I have an arthritis problem, weight bearing exercises (standing up on the bike) results in pain. If you are using a higher cadence that reduces stress as the lower the cadence the higher the pressure on the knee which of course is equal to higher weight bearing. I always cycle uphill sat down (even if it involves contouring).
Uhmmm think I may have gone a little of topic??
Maybe floats first see if that eliminates the problem if so try clips and see if there acceptable to your knee. Also throw in higher cadence where possible as another check.