The knee is a pretty badly-designed joint. I won't go into it too much here, but you can check out my pontifications on why it causes us so many problems here.
Simply put, the knee is a complex, large (the largest in the body) joint, between the two longest bones in the body, and gets most of its stability from four elastic bands. OK, that might be a slight over-simplification, but you get the idea.
In fact, the levers are so long, and the knee so hard to control, we have to insert an extra little floating bone, the patella (or kneecap), to help the thigh muscles straighten your knee when it is bent.
A simple glance at the injury roster for more or less every sport out there (ok, speed origami and tiddlywinks may be total exceptions) will tell us that the knee joint is vulnerable.
Because of its role in walking, the knee has to 'play nicely' with the foot and ankle below, and hip joint, pelvis and low back above. Many knee problems are predisposed towards (or maintained) by issues in these areas. As mentioned elsewhere on this site, knee pain can also be directly referred from other structures such as the lumbar spine (low back) and hip.