What PC code did you use? Some of them are for free day certificates that you need to surrender at the time of rental. If you just used some random number or one you found online without knowing the terms and conditions, it's entirely possible it was for free day that required a physical coupon (like a Hertz Business Rewards Day certificate).
As you pointed out, a credit card dispute is a slippery slope as you very well could end up on the DNR list. Unless you are certain beyond a shadow of a doubt what PC code you used and what the T&C's were for that coupon, you should just drop it and move on. Just our 2 cents...