This is a known issue with some iPad 3rd generation devices. It has been tested though and shouldn't be harmful to your iPad. If it bugs you I would suggest a nice case.
iPad 3 will run a little warmer that the 2 , it has a quad core graphic GPU (Graphics Processor Unit)
If you play Graphic intensive games , this is when it will get warm
Charging while you use it is another instant when it is warmer than usual
Charging while you use it when playing Graphic intensive game, EVEN warmer
Some iPad Cases restrict cooling , remove case and see if this helps.
if the 3G is on when navigating it will be a bit warmer, in fact gets quite warm.
Usage in a hot climate will add to all the above scenarios.
the iPad has an automotive over heat shut-down , if you see this refrain from using especially if in a hot car