Voyager overused the Borg, and that helped to make them less scary, but it wasn't entirely Voyager's fault. The problem began with I, Borg and Decent; showing the Borg as individuals completely nullified any fear we had about their big scary collective. They were scary again in First Contact, although I do agree that the introduction of the Queen was ultimately harmful. And they were pretty terrifying in season 3 of Voyager; I jumped when Voyager came across the damaged cube in Unity, and that formation of cubes that flew past Voyager in Scorpion was as terrifying as the show ever managed to be.
Then came Seven, and seeing a Borg as an individual every week just ruined the fear everyone had about them. Even worse was the fact that Voyager had numerous encounters with the Borg and managed to survive, even though one cube managed to destroy 39 ships at Wolf 359. Plus, episodes like Unimatrix Zero didn't have an epic feel about them, they just felt like routine episodes of Voyager. The Borg were no longer big, they were no longer scary and they were no longer unstoppable. They became routine villains of the week.
The Enterprise episode Regeneration had many problems, but I am willing to overlook them because the Borg were scary again for the first time in a long while.