I don't think he hates Batman, but he certainly doesn't respect Batman.
Superman getting affected by Kryptonite was fine, and totally in line with the character. And he wasn't mind controlled, but Atom found a way to manipulate him. All of that happening was in line with the character and his flaws, knowledge, personality etc. I.e. none of it was out of character.
That isn't the case with Batman as written by Johns, who has unmasked in public, allowed Lex to pick pocket him and unmask his identity...., all of that is out of character because he is meant to be obsessively cautious and aware as much as he is possibly of all of his surroundings. He should have expected Luthor would suspect he is Batman for example.