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”).