Camera rotation is your best friend. If you get used to using it then you will have no problem.

Wait what? Arrow keys?

Honestly, the Rooks is supposed to be pretty big. He's an extremely powerful character, and the game explicitly states that one of his downsides is being a big target. That being said, maybe they can implement something like in the Command and Conquer games, allowing you to see and terget enemy unit silhouettes through him.

Yeah I think it is just an all around targetting issue. At some angles you can have the cursor on a demigod and not be able to target. It seems if a smaller demigod is in front of the rook the smaller demigod becomes almost impossible to target.

True maybe only on mouse over the area though. It would look funny otherwise.