The number one cause of rattles is incorrect reassembly and/or damage to clips when interior bits are removed for adding aftermarket "upgrades" like stereos etc. or by paintless dent removal folks etc. Even dealer mechanics can be a problem if they are not very thorough.

My Carrera had an aftermarket stereo when I bought it and the car made a few noises that bugged the crap out of me. Went through everything between the stereo and the speakers and eventually everything was cleared up and the car is now tight as a drum. I was surprised, as I originally thought some of the noises came from different places.