Naomi is in charge of bringing rebellious angels to heel, by brainwashing them using some kind of drill, reading their thoughts the whole time they're under her control, and making them follow her orders, without them realizing it. We know that she has done this to Cass over and over again. Now consider all those seemingly emotionless Mooks that show up all the time. Consider Anna. How many angels on the show have been brainwashed by Naomi, and how many times?
Castiel: You've been in all our heads! That's the problem!