That's one of the first hypothesis discussed in the article: our brains aren't getting smaller because we are getting dumber, but because the wiring is becoming more efficient.

I think the most interesting part of the article comes at the end, where the author points out that while brain volume has decreased since prehistoric times, it's recently been on the rise. That trend corresponds well with the availablity of protein in human history. Since farming began, protein has been a privilege of the rich. Only recently has it been widely available, and in such quantities. Hence, modern Americans are something like 3 inches taller than their ancestors 150 years ago.