An even easier way to do this is to open your rendered animation in a video editing or compositing program and just key out the background color. Done. Then you don't have to fiddle with it frame by frame. It's often better to render using a green or blue, but you can have good results with many different colors, all depending upon what colors are in your "safe" area. There are many programs that can do this. Premier, Final Cut Pro, After FX, just to name a few.