In the comments of the article I posted there is some discussion about proper seat installation. I thought this commenter summed it pretty well:
"While it may be possible that an improperly installed car seat may not be any more effective than a seat belt alone, and that probably accounts for at least some of the Freakanomics data, that is a SOLVABLE problem. Ditching the car seat is one “solution,” but I would argue that a much better solution would be to meet with a child passenger safety technician to make sure your car seat is being used in a manner that would keep your child as safe as possible. “Other people don’t use car seats correctly, so I won’t use one at all” is a rather absurd conclusion, don’t you think?"
That point aside, the bigger one is that they concentrate on fatalities more than injuries, where there is a ton of data on the effectiveness of seats for children older than 2.
Generally speaking, Freakonomics does raise many interesting points that make you think more critically about causality. But more often than not they end up drawing a blanket conclusion that is as lazy and un-nuanced as the one they claim to have debunked.