I had the same thump everytime I'd hit a big bump, I just layed some carpet under, behind and on both sides of my spare. Cut out a hole for the connection area and havn't had a bump since. It seems to be much quiter back there and it only cost me like $9.99 at meijer for auto carpet that seems to match ours.

BTW, I do still hear the rear seats rattle alittle, but its definatly a different noise then the spare thump.