"How did the ideas about human sexuality become so difficult for religions to deal with?"

My honest opinion? Males dreamed up religions and males cannot stop themselves from putting the sexual act at the centre of everything. Positive or negative, it doesn't matter. We're still living with it. It's why Roger Ailes could tell his female anchors with a straight face, "You'll never get anywhere in this town without letting me ---- you." 

Compare this to: "She does not share her body with a man" and therefore, she will never reach her full "potential." And tell me if there is really a difference. Because I don't think there is. Shocking, I know. But not nearly as shocking as what religion has done to women generally. 

Anyone who thinks God designed that has a hole in the head.