I was in the same boat....! I just got a 2013 Raptor and I was freaking out that I was getting this kind of rattling from a new truck!!!
So I dedicated an entire day to this problem. At first I thought it was the speaker grill. Took of the door panel and secured it down and put the door back on. Still rattling......…
Next I got a thin pole ( like a broom) and taped a good bit of electrical tape on the end (so as to not mar the door) and started poking around on the passenger door. Come to find out I got the door to stop rattling when I pushed the pole between the bottom of the door and the thin running board that covers all the wires. After that I made sure I put the door back on tight(it was). Again
Long story short, it's the door seal on the truck side rubbing the actual door.... Creating a noise that sounds like rattling but its just the most annoying squeaking sound known to man!
To do a quick test to see if this was my actual problem, I used some blue painters tape and taped the area where the door seal comes in contact with the door on the bottom side. Did a rattle free test drive to get a celebratory 12 pack on a job well done. Cracked one open as I used some armor all type stuff and rubbed the seal down. Hasn't rattled since!
Hope this works for all of you.