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!