I have noticed this as well, and I agree it is very overused and cliche. However, I believe it can be done alright.
I actually decided to play with this trope when making my character, Amazon.
Amazon was raised on a bile farm (In China and Korea they farm bears for their bile to be used in traditional Asian Medicine). She finally was given the chance to escape one day, and eagerly took it. Amazon didn't think much about humans after that. Yet the wilderness was much to harsh for her, and she was near death when she was found by a kind old man. This man was a Scientist, working on a revolutionary new drug. A drug involving nanobots. The old man loved nature and decided to try and save the bear using his medicine. And it worked. However, the nanobots where programmed for humans, not animals. And in the process, Amazon was given human like intelligence. With her new intelligence, Amazon found she needed a scapegoat for all her problems in life...and humans fit the bill.
Amazon for a while turned into a sort of terrorist, destroying human property and killing humans for no good reason. She had an organization on her side at one time. Eventually she began to realize what she was doing was wrong, and her efforts fell apart.
Now she has mixed feelings on humans. She still hates them with a passion, yet she owes them her life as well.