This is a conspiracy theory I came up with on why there is no humans in Zootopia. In zootopia they frequently mention how predators and prey have evolved to coexist with each other.
This leads me to believe they rebelled against the humans. Think about it, they were starting to comprehend everything and were becoming intelligent. They were realizing what was happening to them.
They rebelled and killed every single human, and they started an animal society.