I don't think it is fair. Especially because it skews perception of the animals in other literature, and in real life. It's rather arbitrary, and understandably stories need antagonists, but really all animals, like humans, can be good or bad.
Most everyone is famous with the "Big Bad Wolf" in the The Three Little Pigs, and Little Red Riding Hood. This negative portrayal of wolves led to them being hunted to the brink of extinction in Europe and North America. It took a long time for them to recover. While the reputation of the Wolf is somewhat deserved, it isn't really fair when wolves can be good too. In The Call of the Wild, White Fang, and The Word and the Void, wolves are good animals, whose friendships with humans benefits humans immensely. In The Call of the Wild, Buck's connection with wolves avenges the death of his master. In White Fang, the title character saves his master from an otherwise fatal mauling. In The Word and the Void, a wolf protects a young woman from very dangerous creatures.
The Owl is another one that confused me. I grew up shielded from any literature that had even the slightest mention of Witchcraft. Consequently, my experience with owls in literature had been largely shaped by Disney's Bambi, where the owl is portrayed as a good and wise creature. I never associated owls with the occult, so it surprised me when a Wild America episode about owls made the connection.
In Riki Tiki Tavi, the cobras are portrayed as evil, and the title character is good for saving a human family from the evil cobras. But, Mongooses don't just eat snake eggs. They also eat birds eggs, and they prey on other animals, not just snakes. While Cobras have a fearsome reputation, they can also be used for good. Cobra venom is being studied for its applications in painkillers. Cobras eat the rats that can spread bubonic plague, and other diseases. So only focusing on one aspect of their characters is quite shallow.