Why was Zod not in this?

Because Zod is an overhyped and unnecessary character that really doesn't have much of a place in the greater Superman continuity. He was created for the Christopher Reeve films and has a little bit of overflow to the comics (ironicly, the bulk of his comic appearances were written by Richard Donner) and the movie-inspired Smallville series.
This series tried to stand on its own, and copying Zod would have only served to tie it into somebody else' work,

Give Blood Today
God Bless!

Luthor was a greater necessity for a Superman show, since he is so identified as his arch-enemy. Zod is a lesser figure in Superman history, but had had quite a bit of exposure with the Reeve films and their repeated broadcasts (especially by the time the animated series debuted). I still would have gone for Zod, but that's just me.

Bane was pretty one dimensional in the comics, at that point. To me, Knightfall required Batman to act out of character and for the supporting cast to be equally, if not more stupid. I like how the animated version had Batman just slice open the Venom tubes, when Bane lifts him up to deliver the backbreaker. On the other hand, I liked the lucha libre design, as I always felt the Bane mask had a sort of wrestling look to it (not to mention the idea of super steroids).

Me, I prefer the Lex Luthor of Elliot S! Maggin's stories, especially his two Superman novels, Last Son of Krypton and Miracle Monday (released as tie-ins, but not novelizations, with the first two Reeve films). That Luthor was a complex character, with real motivations and a personality. he had a sense of humor and heroes (Einstein) and considered Clark to have been his only real friend in Smallville (which shaped the Smallville series). He also had an altruistic side, which he practised using disguises and alter egos. he was a crusading doctor, a sculptor (to hide some of his inventions, like a spaceship), and a philanthropist. He was an interesting mixture of a misunderstood and bullied child (by family and outsiders), who layered grievance upon grievance, seeking attention through criminal acts; yet, he still had a beneficial side, somewhat affected by the unconditional friendship of Clark Kent, as teenagers. As an adult, he refused to recognize that Clark had once been his friend, as it detracted from his adult personna and made him seem more vulnerable. Maggin also presented the idea that Luthor's true anger at Superman was not the loss of hair, but the destruction of a protoplasmic creature to which Luthor gave life, in that same fire. It is the death of his "child" that Luthor holds against Superman, not the hair loss, or his interruptions of Luthor's crimes.

"Fortunately, Ah keep mah feathers numbered for just such an emergency!"

I don't think they were considering using Zod in the movies back then. Wasn't Superman Lives in pre-production at the time? The villains in that would have been Lex Luthor, Brainiac, and Doomsday, and we got two out of three of those in the show, so I don't see why there would have been a restriction against using Zod.