When Star Trek: Voyager began, it had built in tension with the Maquis and Starfleet officers at odds with one another. The Maquis were considered criminals, and that was what had started Voyager's journey. The ship went after a missing Maquis spacecraft that had Captain Janeway's [Kate Mulgrew] friend and security officer, Tuvok [Tim Russ], aboard. But once the Caretaker flung the ship so far away from home, the crew of Voyager were forced to work alongside those they considered enemies. But that animosity didn't last long. And fans have often wondered why Voyager writers didn't keep the two factions at each others' throats for a while longer.
In an interview in Starlog's Star Trek: Voyager Magazine during Voyager's second year, Robert Beltran explained that he understood why the writers chose to go in a different direction. The writers believed there was more drama that could be brought about by having the crews work together and focus on one goal—getting home.
Beltran didn't think it would have made much sense to keep the conflict between the Maquis and the Starfleet crew going when there was something more important to work on. On top of that, the Maquis' dispute, which was taking place on their homeworld, was with the Cardassians not Starfleet. So having the two crews come together, even though they both had differing reasons for wanting to get home, helped move the show forward and actually created friendships and built trust that lasted for decades.
Had the Maquis and the Voyager crew remained enemies, Chakotay couldn't have been Janeway's first officer, and B'Elanna Torres [Roxann Dawson] couldn't have become the ship's chief engineer. It would have made it difficult for her to get involved with Tom Paris [Robert Duncan McNeill] as well. So though the fans wanted a bit more conflict between the two factions, it clearly made more sense to have them put aside their differences in order to get back home.