He didn't hate the Uchiha; yes he had some bias towards them because of Madara and the fact that they killed many of his clansmen when he was growing up in the Warring States Period, but he was more afraid of the power they possessed through the Sharingan. He had Uchiha who he held in high regard such as Kagami, Shisui's ancestor, and he assigned the clan the task of running the Konoha Police Force because of their abilities.