Are the humans to blame for the misery of the animals?
In both literature and the actual world this depends to a great degree upon the nature of the specific animals and the specific humans. For example, the novel Black Beauty is meant to raise awareness of mistreatment of horses, and Sewell makes a sharp contrast between good and bad horse owners. In Animal Farm, on the other hand, Orwell has the animals initially place blame on the farmer, but they actually end up worse off under a regime created by themselves.
In reality, wild and domesticated animals live under very different circumstances. In the wild, human-caused global climate change has harmed many animal species. Other species have been driven into extinction by humans, either through habitat loss, hunting, or introduction of alien species that compete with them for food. Among domesticated animals, some, such as cats and dogs thrive in partnership with humans, living far longer than their wild counterparts. Animals used for food, such as pigs, chicken, and cattle, can either be treated well, as in humanely raised and free range animals, or badly, as in factory farms.