This has been bugging me forever! I thought the rear speakers or the cover above the rear seats was the issue but it turnrd out to be the damn tool box! I took it out of the side compartment and put in in the corner of the trunk and no more rattling! I hope this can help someone's frustration.

 

I had this problem before too!

Then I figured out the tool box has a lock that keeps it from moving around.

 

Yeah, I know it has a lock, but for some reason it still rattled. The rubber and felt around the box is all in place too.