Yup. Dukat is obviously the antagonist during the occupation arc in S6, no viewer was dumb enough to view him as a hero there. Still, he was written as multi-dimensional with his genuine affection for Kira and his daughter being obvious. I can think of Dukat as a monstrous douche for betraying the Alpha Quadrant to the Dominion, while still feeling really bad for him when his daughter bites it.
But the writers fell the need to spoonfeed the audience and make him 2d evil. The exact same thing happened with Winn, who is OBVIOUSLY starting to like and respect Sisko during S5. Then she comes back in S6 as a 2d evil bitch.