...Janeway was/is only one character (and in my opinion not a very interesting one) in a whole ensemble. Go and read the novels by Kirsten, especially the ones without Janeway, and you'll see that this crew, this group of people, are AS good as they are without her, then with.
Everyone enjoys a show in different ways and for different reasons. Please don't assume I enjoy things the same way you do and that everyone else should too.
One of the Treks I grew up on was Voyager and Janeway was a huge part of it because seeing a woman in a role like that as a girl made a great impression on me. So excuse me if Janeway is a huge part of Voyager for me and factors into my choices for enjoying fandom outside the show itself....
But there's a middle ground. I like Janeway, I think that for the most part she was a great female role model, but she was still just the lead character in an ensemble, not a solo heroine. No matter how important she was, she still wasn't the only worthwhile character or element to the series.
Back in the days when there was only TOS, Spock was by far the most popular character, the one who overshadowed all the others in the eyes of the public and many of the fans. But Spock died in TWOK, and the DC comics that followed had to carry on without him; even after he was resurrected, DC had to keep him marginalized for the most part because they didn't know where the studio would take him in the next film. So for several years, the TOS comics proceeded without Spock. Yet they still told worthwhile and engaging stories and found a way to adjust to the change. It helped that Spock's legacy (in the person of Saavik, and in the ways his friends and colleagues had been influenced and affected by their interactions with him) was still a strong part of the stories, even without him being physically present in them.