McDougall's basic premise is that we were faster and less injury-prone before we started wearing all these fancy running shoes and that they are what's causing running injuries. For example, in the New York times article:
"Back in the ’60s, Americans 'ran way more and way faster in the thinnest little shoes, and we never got hurt,' Amby Burfoot, a longtime Runner’s World editor and former Boston Marathon champion, said during a talk before the Lehigh Valley Half-Marathon I attended last year. 'I never even remember talking about injuries back then,' Burfoot said. 'So you’ve got to wonder what’s changed.'"
Statistics frowns on such anecdotal evidence, though it does make a good story. Did we really run faster? There are a lot of facts that we can look at though average times aren't among them. Marathon records (shown in Wikipedia) for men have indeed only downticked a little since the sixties. In 1970, Ron Hill of the UK (close enough, runnig-shoe wise, to be considered american?) set a record of 2:09:29. This year, a new record of 2:03:38 was set (the most recent US record was 2:05:38 in 2002). Six minutes in 40 years doesnt seem like much, but is it because of the shoes or because the sport has matured? And are Americans seen less because running isnt really a big competitive sport here?
When you look at women's times, the changes are much more dramatic. Women more recently began running marathons and fewer participated in the sport in general until relatively recently. In 1970, the women's marathon record was 3:02:53 (set by an american). In 2003, Paula Radcliffe (England) ran it in 2:15:25. That's a 47 minute improvement, or nearly 2 minutes per mile. In the 2011 New York Marathon, 40 women from the US bested the 1970 record time (see marathon site here for results).
So, I can't agree that we ran "way faster" 40 years ago. This doesn't mean that bare foot runners are slower than shoed runners because changes over the last fourty years in the level of competition, and improvements in training and fitness, rather than shoes, might have been the factors contributing to improved times.
How about injury rates? Do people get more injuries with running shoes than without? Unfortunately, any data on injury rates is tainted by the changes in the makeup of the population that runs (from a small, highly fit population to a large more population more varied in fitness--think of the then-overweight President Clinton running with a stop at McDonalds post-jog), and there haven't been any studies that directly compare injuries over time for barefoot running against running shoe running. A good summary article is here.
A recent article in Nature, while not looking at historical data, supports McDougall's contention that running shoes can be more harmful than bare feet when running. The article is lead-authored by Daniel Lieberman, a big advocate of barefoot running, so his bias may have been to look at things he believed were helpful about barefoot running and not at aspects of barefoot running that may be harmful. The article looks at impact forces and not at injuries, and doesn't consider that runners with shoes may be able to change their stride to reduce the impact forces (McDougall says this is hard to do with running shoes, and, from my own experience, I tend to agree, though I don't think it is impossible).
The statistical net-net is that there is no direct evidence either way right now. I admit some bias but I would say that the lack of evidence, given the power and money behind the shoe industry, tends to make me believe that, at best, fancy shoes are no better than bare feet, because if there were an effect in favor of shoes, I would certainly think we'd have seen a study by now (this is something correctly pointed out by McDougall and other advocates of barefoot running). Therefore, don't be surprised if you see me running with feet au-naturel someday soon.