Head honcho Ronald D. Moore commented on the frustrating convenience of replicators in "The Science of Star Trek: The Scientific Facts Behind the Voyages in Space and Time."
Moore was concerned that replicators robbed writers of their ability to write drama — if every object can be replaced out of thin air, then there are no needs.
This convenience may be why replicators have additional limitations such as using a lot of energy: it's not interesting for viewers if a replicator can solve every problem.