I know the transporter was initially, when budegts were low, a tool to avoid having to shoot costly spaceship landings on planets, but they soon evolved into a frequently recurring item, part of fanlore, and a major plot element in the many episodes where a transporter accident causes things to go wrong. But they (and together with their close siblings, the replicator) cause major plotholes and inconsistencies. To name just a few examples:
There are episodes where some scarce resource is traded. The resource can be delivered to its destination via transporter. I would imagine that a civilisation that has transporter/replicator technology would not have a need to engage in trade to obtain such a resource; the fact that you can transport it shows that you have devices capable of synthesising the commodity from energy whenever you need it.
Some episodes establish the practice of the Enterprise to carry spare parts for its engines in case repairs are necessary. I would imagine that, again, a civilisation with transporter and replicator technology would not need to haul around physical specimens of such spare parts. All you’d need is a record of the information that would be sent to a transporter when you transport it, and then you can synthesise it when needed. Would save you a lot of storage space during your voyage.
The transporters have “bio-filters” which filter out viruses and other pathogens when people are transported, to avoid a contamination of the ship when they are beamed on board. But once you have that, there is no reason why you shouldn’t use the same technology on someone who is already on board and infected with a pathogen.
My impression (after seeing only one season each of TOS and TNG) is that the whole transporter/replicator thing was never thought through by the writers, and is always capable of doing exactly what is needed to drive the plot of the episode in question - no more, no less. Or have there been attempts made to explain these and similar inconsistencies in a somewhat satisfying manner?