Hello guys!
I don't known why, but all villages hate wihout any particular reason. During the character creation I choose Dragonstone/Rhollor, so I initially thought the reason was my religion. But the villages that follow Rhollor also hate me.
After I converted myself to the faith of seven the villagers are still hostile towards me. Actually, their hate towards me keeps increasing.
Same for me in 4.1
Try updating to 4.1, Produno fixed it. If it's still not working then it could be your actions. I've found that raiding villages and caravans can universally affect village relations.