The Fat Boy Program simply is a derogatory name for what is now called the "Fitness Enhancement Program" by the Navy. Being assigned to the "Fat Boy/Fat Girl Program" was and should be something to be ashamed of, unless you are on your way out of the service and just don't care.
In short, it is simply mandatory remedial physical training to help you bring your Physical Readiness Test scores up as well as help you remove the weight so that hopefully when you step on the scale you are within standards.
There are a plethora of exercise programs and diet programs out there designed to help folks get and stay within standards. Before starting any of them talk to your doctor.