simply the defender ducked his head. Yes, he also hit him with the shoulder, but the crown of his head hit the other person in the head. It's, by rule, a flag. It doesn't matter if the runner is 5ft tall or 7ft tall. It's all about the defender keeping his head up.
Now, if he had his head up and hit him with his facemask, then you have an argument...although, the point of keeping your head up is to see what your hitting and theoretically being able to avoid hitting the other player in the head.
This part of the rule is a continuation of what everyone is taught when they first start playing football. Tackle with your head up. We can get into all kinds of nuanced parts of tackling, but this part takes much of the guess work out of it for officials (did he mean to do it? Did the runner duck? How tall is the runner? At what point did the runner lower his head? ect...). It's just a simple, "was his head down and did it hit the other player in the head?"
It sucks, but if it was our guy knocked out by a Dukie, we'd be sure it was a good call.