Quantum Teleportation and Molecular Replication
The transporter and replicator technologies appear similar to the outside viewer. Their effects resemble each other, appearing to create or move something from one place to another, indeed replication may have led to the more advanced transporter technology with the creation of quantum manipulation technologies such as the Pattern Buffer and the Heisenberg Compensators. But in this case, the issue is both one of power required to manipulate matter and the other is selectivity and data storage required to keep information about the matter in question being replicated.
The Transporter
The transporter manipulates matter at the atomic and quantum level. Literally every aspect of matter is held, gathered, analyzed and stored at the quantum level until the material is moved. This is both an energy-intensive and computer-intensive technology that references a real quantum subject and displaces that subject in a matter stream and then reconstructs the target.
The transporter might be more of a matter-displacement device, transforming the matter into an energy stream to be reconstructed or returned to the default matter state upon completion of the transport. This would explain why energy shields or ion/electrical disruptions prevent the matter-stream from being effective. It would also explain why the transporter could not (normally, until the recent Star Trek 2009) transport to a ship in warp. The matter stream was limited to the electromagnetic spectrum and the speed of light. The carrier field is delicately balanced and the quality of the signal even having the slightest variance could be dangerous to the viability of the subject transported.
The Replicator
The replicator is a molecular technology that is capable of taking source matter and converting it into the molecular compounds that are capable of being recreated using the molecular information stored in the Starfleet computers. Since the quantum information without a source would be exponentially greater, the replicator does not attempt to recreate perfectly any matter produced in it, hence the flavor issues with food as molecular compounds may less than perfectly modeled. They would be fine for consumption as safety protocols would not allow inedible matter to be created, but the taste quality might be detectable to the sophisticated palette.
Since replication is an imperfect process, it explains why certain compounds, or physical substances may either be resistant to replication or leave molecular traces that could render the object less perfect for certain kinds of work or questions of purity may make it unsuitable for the creation of currency models such as latinum which may include quantum information to ensure its "purity".
The Difference
The Difference
The transporter is manipulating information thousands of times more complex and requires technology that currently cannot even be conceived of such as the "Heisenberg Compensators" which would make it possible to know everything about the quantum state of a particular subject being transported. But for the transporter to do its work, it must have a real subject whose quantum state is being manipulated and transported. It is this quantum field state that the replicator is simply incapable of analyzing or creating when it performs "molecular replication"
Both technologies are unfortunately shown being capable of doing a variety of things for the sake of plot and stories making them more often "deus ex machina" than reliable technologies that can be taken apart for scientific accuracy.