Okaaaay, just because you've brought it up…
Transporters in Star Trek are shown to definitely not be duplication machines. "Our Man Bashir" (DS9) is probably the most definitive proof of that.
Personally, I think transporter technology explains the staunch atheist (but still open-minded and sometimes spiritualist) Federation mindset: they know that their entire being can be reduced to a matter/energy stream. The transporter makes a devastating philosophical challenge to the idea of a "soul." Which is, ironically, why so many Federation officers refuse to accept anything that challenges that assumption (VOY "Sacred Ground").
Uhhh, excuse me? My takes are totally original. T'Pol told me so.