I had this published in a magazine article awhile back, thought you might enjoy it.
Death by Transporter
by Michael Bradley
For Star Trek fans, the transporter is the key to most away teams. In space dock you might use the shuttle and certainly if the transporter is blocked by shielding or other devices you would use the shuttle. How many times have we seen the transporter used throughout the series, and the only one smart enough to question this was “Bones”, Doctor McCoy. He complained that breaking a person down into individual atoms and beaming them across space and reassembling them was “unnatural.”
The sad truth is that the transporter is actually a death device that produces a clone. Each person entering is disintegrated into nothing but a computer pattern duplicating their original mass. Those actual particles are not sent through space, which could not happen at warp speed, much less sub-light. The computer projects the image of the person into the destination and assembles atoms to reconstruct them.
Every time Captain Kirk, Spock, or anyone else stepped into the transporter, they died. A perfect clone, which “thinks” it is still the same person, was then created. Even under the best circumstances, repeated death and re-cloning will get some of the pieces wrong. Theoretically, the more times you go through the transporter, the less you will be like the original. There have been episodes where people were merged, mangled, or had the “anti-virus” program remove alien life and microbes from the new clone, leaving behind part of the original.
The official protectors of the Star Trek brand deny this is the way transporters work. They say that it breaks down your molecules then converts them to a light beam, then reassembles them. This cannot be true, given the Star Trek canon. Every trekker knows you cannot beam someone through an active shield; however, lasers, photon torpedoes and phaser banks CAN go through a shield on the way out. So if light, energy and matter can travel out, why not molecules in a light beam?
Further proof that the transporter disintegrates the occupant then creates a clone is found in Star Trek: The Next Generation episode entitled “Second Chances” in which Commander Riker is duplicated twice. One version goes up to the ship, while the other is stranded behind. After that, they diverge in personalities based on their experiences. If in fact, a transporter only uses the original mass of the individual, then two Rikers would both only be half complete, and both would be dead. If it disintegrates and kills the first Riker, then accidentally puts them together twice in different spots, that would explain the plot.
Star Trek has extensive usage of the replicators. Captain Picard says, Earl Grey hot, and voila, there it is. The replicators basically take inert mass and energy and remake it into whatever product is desired. The transporters are simply replicators that project their product, destroying the original, encoding it, then using target mass to create a replica.
If you believe in souls, or even personal identity, this is of great concern. If you understood how a transporter actually works, would you ever step into one? Would you be willing to die each time, knowing a clone of you, who thinks they are you and acts like you, will be created on the other end? Personally, there is no way I would do it. Space is risky enough, and you could get me to serve on a ship. Walk into a death chamber to die and be cloned? I’ll pass, thank you very much.
FOLLOW 
Michael Bradley - Time Traveler 