I dunno. I'm relatively convinced that they could replicate a bee if they really wanted to, it's just too power intensive for its purpose (you get: a bee). It's only a machine made of chitin and goop. Marvelously complex technologically, but nothing as complex as a human brain.
At any rate, I think (TNG TM aside) that the transporter/replicator distinction is that the information used to recreate a human body, swarm of bees, humpback whale, test cylinder, Tom Riker or whatever is somehow encoded in the disassembled object itself. Theoretically, this could be done by an external computer, but if a transporter truly organizes matter at such a resolution that the precise position and velocity of individual atoms are known, the only physically possible storage method I can think of is at least the size of the body itself. Indeterminancy may dictate that such information can't be known without interfering with the particles, the transfer of information being a physical process that affects the position and/or velocity of the particles in question. At the same time, a quantum system appears fully capable of computing itself in a satisfactory manner, insofar as anything manages to exist from one moment to the next.
Now here's a silly transporter question: why is the sensation of being transported not atrociously painful? The body is literally disintegrated by the transporter beam, and generally that sort of thing hurts. Do they beam out the central nervous system first and put it back in last?