Janeway was a bad Captain because the writers tried to make her a strong woman. And that never pays off. Same thing happened with Judi Dench's M in the new Bond films. Or President Roslin in nuBSG. They want them to appear strong and determined, and somehow that means that they make bad, morally questionable, controversial decisions. As long as they are tough while making those decision, it's fine.
Janeway is wrong so many times during the show it's not even funny anymore. She sticks to her wrong decisions until almost everyone disagreed with her and tried to talk sense into her.