Think of it this way... They beam Capt. Kirk down to the planet... That means the original was destroyed on the pad... What is on the planet is only a copy. When they beam him up the copy on the planet was vaporized and now you have the copy of the copy...

James T. Kirk was lost the first time he was transported. The transporter is not moving the original.

http://www.popularmechanics.com/culture/tv/a19793/the-trouble-with-the-star-trek-transporter/