However, as he states in the article, instinct is the result of experience. He is saying the mechanism of instinct is older in humans than logic, so the process is more refined/trustworthy when comparing the two. Seems right to me..
However, there have been billions of bad-instinct decisions as well, ranging from "should have zigged instead of zagged" while driving a fast car around a curve to Napoleon invading Russia.
But, if instinct trumped logic as the author suggests, humans wouldn't be at the top of the food chain and driving cars.