Chakotay did challenge Janeway a couple of times, but she just steamrolled him. Look at "Scorpion, Part II", when Chakotay dared to defy the wishes of the all-powerful Janeway by ending the alliance with the Borg, she relieved him of duty and locked him up in his quarters.
That happened in "Equinox, Part II."
In "Scorpion, Part II," she listens to Chakotay and sets up contingency plans in case Seven actually tries to betray them. That's why Chakotay is "hooked up" and waiting for her to delare "Scorpion." So, in that episode, she listens, too, but the changes happen off screen.
I don't understand why Janeway is "labeled" as a captain who doesn't listen to her crew, when she does, many times. It seems to me that people just don't pay very close attention to Janeway's actions, or perhaps just don't remember those times because they are more impressed by the other times when she steadfastly refuses to budge. The one that sticks in my mind is when she refuses to drop Starfleet principles when the ship is in "The Void." In that case, she was right and managed to escape by making friends instead of raiding other ships.
Oh, she also listened to her crew when they suggested that they ally themselves with the Trabe in "Alliances," which turned out to be a terrible mistake. Sometimes, the captain just might be right to ignore the crew's advice!
You might be right AuntKate, that was just my recollection from watching Voyager
when it was being broadcast and upon buying the DVD boxsets a couple of years ago. Hopefully, this rewatch will change and inform my opinion.
But I do think that Janeway was more isolated in her decision making, yes she was challenged on occassion and sometimes bowed to those suggestions. However, I might be wrong, but she seemed to do it less so than either Kirk, Picard or Sisko before her.
Kirk often sought the opinions of Spock, McCoy and Scotty, an on occassions when he went off on his own, especially "Obsession", it was viewed to be the incorrect course of action. I would have liked to see more of this from Janeway, but I suppose TPTB thought it would weaken her, the first "main" female captain in Trek
. A real pity.