In the Bill Theiss book "The Making of Star Trek" I remember the reference to having matter transmission devices on ships at the level of technology otherwise displayed in Trek was akin to Cleopatra's barge on the Nile packing an electron microscope. The transporter concept was a product of limited effects budgets and dramatic pacing. A camera trick involving sprinkling aluminium dust was much cheaper and moved the story along faster than a shuttlecraft landing sequence (and the full-size shuttlecraft mock-up hadn't been completed before the pilots and first episodes were shot).
The most recent plot-driven abuse of the transporter concept was CumberKahn's personal device delivering him to the klingon homeworld after shooting up a few fed big-wigs in ST:ID. I guess Section 31 got hold of some gear from someone like Gary Seven's mates.
Just to be clear - count me in the "transport is murder" camp, if for nothing more than the sake of technical consistency.