I think Edelgard is hated because, for the right or wrong reasons, she did start the war. And in most of the routes in the game, the task falls upon you and your house to face her and put an end to the war that SHE started. Still, I would hesitate to call her an antagonist, because her attack on the church and what it stands for is partly justified. Also, Edelgard was still against those who slither in the dark, who are the true enemies of FE3H. Yes, most routes do depict her as an enemy, but with the exception of the Blue Lions Route, she is not the main enemy (Edelgard is the main antagonist of the Blue Lions Route). Whether or not Edelgard is an antagonist is, in my opinion, dependent on which route you like most. If you loved the Black Eagles Route, then you were probably cheering Edelgard on throughout her campaign against the Church of Seiros, but if you were more of a fan of the other routes, then you saw her as a traitor to the peace of Fodlan, and killed her during your playthrough.