To answer your question if it is the portly charger then its just the age of the charger. If it the slender charger meaning the piece that hooks into the usb cable then you have a loose connection in your usb cable it has happen to me during the life of my original ipad .
It does get warm, but if it's too hot to handle, then something may be wrong and you should stop using it. If it's within the first year it'll be covered under the warranty if it's a manufacturer's defects. You can take it into your local apple store and have them take a look at it.