I think the reason why they are using Zod is because Superman as a character isn't cool and a total reboot with absolutely no connection at all to Donner's world is a really hard sell, even with Nolan aboard. I am not saying they are going to acknowledge Donner's use of Zod at all, but just having a familiar villian (if they are not using Lex) is probably a smart thing from their point of view.
Batman is different and I think that character will always do well for the most part (unless it's Clooney and nipples). I think a a new director could continue/reboot Batman after Nolan and it would still do big box office, because people love the character. He is certainly more marketable in movies over Superman anyway.