There are times when Janeway listens. Chakotay spoke up in "Unimatrix Zero," refusing to support her desire to go to the Borg alone, and Janeway revised her plans. In "Night," the crew defies her when she suggests staying behind as the ship escapes. Again, she modifies her plans. In "Year of Hell," when Chakotay suggests that it might be time to abandon the ship, she doesn't disagree, she just says, "Not yet." In the episode "Omega Directive," she abandons her Starfleet orders and lets the crew help her deal with the problem. So, yeah, she does listen.
What we see of their interaction focuses on times of conflict, because that is what is interesting. However, I think they might have worked more closely on some plans than was ever shown on the program. There were probably many (unfilmed) times where he confronted her in the planning stages and influenced her final decision. To show that week after week would have been deadly dull.
The real relationship between Janeway and Chakotay is largely undeveloped. In later seasons, their interaction is often filmed as they walk through the ship, for some reason. But we know that they met regularly after hours for meals and that they probably talked through situations and scenarios in exhaustive detail. One thing I've noticed is that they almost always have fallback positions and contingency plans in place ahead of time.
Of course, I'm talking about the series here, not the book. Haven't read it.