Is Progressive your insurance company or the guy's who rearended you. If it is yours, then , as far as the aftermarket parts goes, I bet if you look in your insurance policy "small print" it will mention using aftermarket parts. My insurance co. (State Farm) was sued a few years ago by a class of policyholders because of their policy of using aftermarket parts. Now the policies specify that aftermarket parts will be used when available. I would be surprised if other large insurance companies havent followed suit.
NOW if Progressive is the other guys insurance, then you should be able to get it fixed like new, you will probably need an attorney, though. This way, you will basically be dealing with their insurance company (thru an attorney, get one). SEARCH OTHER MESSAGE BOARDS, ESPECIALLY MOTORCYCLE FORUMS, FOR OTHER PEOPLE IN THIS SITUATION. YOU SHOULD FIND A LOT OF INFO THAT WAY, MOTORCYCLES GET REAR ENDED A PRETTY GOOD AMOUNT AT LIGHT, AND IN TRAFFIC.
Progressive is in the business to screw you(make money), so they are going to pay out the least possible. If you have a police report and it is clear cut that you were rear ended and who was at fault, you should have no problem getting a good lawyer to go straight after the other guys insurance company for whatever you need to fix the car, plus medical, pain and suffering (if this happened in this case).
Good Luck!
Edited to add that I wasnt sure who's insurance company was Progressive.