Temperature while charging

Because car chargers work at a different voltage.

No, it has more to do with the type of charger, the amount of voltage/amperage and what its rated for. Not all car chargers work well for every phone. I've gone cheap and I've gone slightly higher end and the difference was clear to me.

Every phone i've ever had has gotten warmer charging with a car charger, whether it be an oem or aftermarket.  Car chargers in general charge the phone faster,(higher output) which accounts for the extra heat.

And you would be correct.

While he's correct about the different voltage It's not the reason. While charging in any way the volts are converted to the correct amount needed for this phone, otherwise you would fry it the second you plugged it in. I had the same issue with my first original EVO (4g), most of the time I felt zero heat while charging it but sometimes I'd pick up my phone and it would be so hot it almost burned me. This happened to me on both of my first EVO 4G's at many random times. I've had my EVO 3D for a month now and it's happened a few times as well. I have 4 home chargers (3 of the 4 original HTC brands, 1 off brand), and 3 car car chargers. I've never isolated to a specific charger, it's happened on all of them at one point. So that makes it the phone itself that has some problem. I don't know that it hurts the phone but I have to assume being that hot can't be good for it. When I notice it I take it off the charger, give it a few minutes, and start over. That's been the only fix I've ever found.

are you guys/gals sure you aint running some crazy app in the background that is making the processor heat up while charging?