Oz seems like he's been held against his will and tortured somewhat. A lifetime worth of brainwashing and torture is bound to affect a character's original motivations. It's likely that Manhattan whisked him away and proceeded to corrupt him. Manhattan's goal here seemed to have been to target the parents of Superman and Batman to help him push them out of wanting to be heroes anymore.
We know from an interview released after "The Button" crossover that it was always Manhattan's intention that Thomas Wayne would suggest to his son to stop being Batman. That's why he sent Batman and Flash back to to the Flashpoint reality. His tactic here seems to be to have Oz remove Clark's faith in humanity and in turn Jor El's intention for Clark to lead the species by example. Manhattan wants Clark to lose faith in humanity as a whole (with the exception of Lois and Jon), thus questioning his role as Superman.