I think there is something unique about consciousness that science is of yet unaware of. It may be more than the sum of its parts.
Take identical twins for example. They are identical in all aspects. Yet they have seperate conciousness. They are not interchangeable. If a theoretical transporter is nothing more than a twin-machine, then there is a very good possibility that the original is destroyed...along with it's unique consciousness, and a duplicate produced, with an identical consciousness but not necessarily that of the original person. Heavy.
That uncertainty is why I wouldn't want to use one of those things!