I just detailed my best friend's Jeep that I'm selling for him, and I used Hot Spot to take out some pretty set-in stains on the headliner. It did not discolor the felt, so I assume it would be okay on carpeting, too; but like they say, "Test a small hidden area (under a seat) first!"
Then, there's always the old trick of cutting out the rust stained area if it's not too big, the cutting out a section of carpet from under a seat and gluing it down.
FGTB