Been using two Rezound batteries in my Thunderbolt since Nov. 2011, but they're typically charged via an external Seidio Multi-function battery charger. On the few occasions I've charged them via the phone (with the stock charger) or via USB cable to a PC, the only anomaly is the charge level will jump from approx. 80% to 100% very quick, otherwise no heat issues.
Haven't tried a car charger for quite a while. Were you using the phone at the time while it was charging (ex. Navigation with GPS enabled)? That will cause increased heat build up. There's also the possibility the car charger isn't working properly. I'd recommend a high quality Motorola charger such as this one: