Caesar is our protagonist and he is at the core a "good" character but even he explored a darker side in WAR. Yes, we tend to root for the apes in this trilogy but that's mostly because their leader is so good. We certainly weren't rooting for the apes in DAWN after they had taken over the human base. With Koba at the helm they were the "bad guys". Even then, with every "bad guy" in this series we understand their intentions and almost sympathize with them.

This series was such a nice break from the current trend of superhero movies that have a clear-cut good guy vs bad guy story. Some try to give the bad guys a little depth but ultimately it's just good vs evil.