ReeceZ,
Top Rattle & Vibration
Click the link. Its a thread from this forum from way back in 2012, and at the bottom of page 2 of this thread a guy posts pictures of the tonneau cover rests that can be adjusted to align the cover when closed. If the stops are incorrectly adjusted, they may be the cause of your rattle.
You should read through the entire thread (all 3 pages) since there may well be other ideas in there you can try as well. Good Luck!
Gene