Chances are its the inspection plate between the trans and engine, or you are missing the 2 bolts at the bottom of the inspection plate.
I have the same issue, I brought the car to the dealership and they replaced the inspection plate with a "new and improved" plate, they also put the 2 missing bolts at the bottom in, the noise went away for a couple of days. Started it up the other day and the rattle is back, not quite sure what to do now. Starting to wonder if it is the throwout bearing?
When i first start it it rattles regardless if the clutch is pressed or not, but as it warms up pressing the clutch in sortof makes the noise disappear.
I only have 23,000 miles on it so far.