Here’s a great Final Cut Pro video tutorial on how to hand-track a blur filter to cover up a person’s face or object.
The particular effect is designed for a quick work-around for those who need to track a person’s face, or perhaps a license plate of a car. It’s down and dirty, but yet does the job. For automatic motion tracking, you can certainly use Apple Motion. However, I think you’d find it’s probably easier to create the effect manually within Final Cut Pro.