I don't think anyone can say defnitively why injuries have increased. Also, you've got to be careful with headlines as the number of knee injuries will increase if an increasing number of people start running. Its only significant if the percentage of runners suffering knee injuries increases, and these knee injuries are directly attributable to running. I'll admit to a personal interest in this as I'd classify myself as a runner and was out for about 9 months with a knee injury. The knee injury was the result of a cycling accident, and was unrelated to running - but would I have been include in the program's stats?.
I don't understand the "suited to running" argument, as its something many adult friends & colleagues have said to me since I started running. However, when my young kids are at parties etc, I never see any of these children saying they are not suited to running whilst sprinting round the room. In my opinion, this is probably due to our bodies adapting to modern life, which involves more sitting than standing/moving, but with a little work (core strength & stretches etc) that majority of adults could adapt back to their childhood ability to run pain free. There are adults who can't run, e.g. one colleague has a damged knee from his rugby playing days, but I suspect they are a minority of the adults who say they can't run.
I think its in the "Born to Run" book that did have one interesting statistic, where one study of runners in a particular marathon found that there was no correlation between injury rate and the amount of training miles run, but there was a correlation between the injury rate and the cost of the running shoes. So you were more likely to get injured if you spent more on your shoes. It would be interesting if this finding could be corroborated, and whether other factors could be eliminated (e.g. do people who spend more on shoes walk less, or are they more likely to train beyond their current ability etc).