My Honda Element has a rubber floor too and also gets quite hot. In fact, on a long trip, my dog prefers the seat as the floor gets too hot.
Here is my take on this.
Rubber acts as an insulator for hot and cold. Look at those things you put your beer/soda can in to keep it cold longer. Also, rubber does not breath...hence, plastic cups.
So you have a metal sheet (the floor) with hot gasses flowing along one side of it and a rubber insulator on top of it. Guess what...it stays hotter because the heat transfering through the metal sheet (the floor) goes no where except for what is absorbed into the rubber floor.
With carpet the heat can escape because it is porous. Even with that foam underlayment some autocarpets have, it is still an open cell foam so heat can escape from it.
1997 Ranger XLT Stepside - 2000 2.5L Engine - Cayman Green - Actually it's running pretty good after new plugs, coils, plug wires, pvc valve and Injectors!!! Runs like a champ!
So, I'll open a homebrew play some Fantasy Football