I suspect it might have to do with encounters against Jem'Hadar attack ships, where some light bulb after reviewing the Odyssey's loss for instance reasoned that small, high powered attack ships would do better against larger ships.
While anybody with any sense would then say "okay, build more Defiants" perhaps someone thought that a larger ship splitting up into smaller ones would gain an element of surprise.
To be fair, we subsequently see mass-produced Defiants (two in that very episode) and the Prometheus never appears again.
It wouldn't be the first time the military has engaged in a costly experiment that yields no real benefit after all.
Message in Bottle actually happened during Dominion War; Prometheus was still prototype and it was impossible to get them on front before war ended, even if serial construction started right after Prometheus was returned to Starfleet. We do see Prometheus class ships on two more occasions - one was part of fleet sent to intercept Borg sphere (Endgame) and another was part of fleet sent to intercept Scimitar (Star Trek : Nemesis). So ship obviously did make it in serial construction.
1) You have one ship which can split in several smaller ships. So that one ship can perform missions intended for both larger and smaller vessels, and when it goes on longer solitary missions it can do things that would normally require multiple smaller vessels.
2) Shields seem to have more troble stopping, say, two 250 MW beams than single 500 MW beam. Along with more weapons that it could be able to bring on bear, it could also play part.
3) Sections are clearly coordinated by central computer, that increases effectivness of such attack.