I've always heard a lot of this is due to improper running technique, since shoe technology shifted to a heavily-padded heel. This in turn made people more likely to land on the heel, which sends the shock right up the leg, into the knee.

Barefoot running, and less padded shoes, promote landing on the balls of your feet (as otherwise it's incredibly painful!). Landing on the balls of your feet allows your foot to reduce the force that gets shot up the leg.