The way I see it, anyone's view on any one or more relationships in Trek (or any other fandom) is completely subjective. Some may see chemistry where others do not. The Janeway/Chakotay relationship (and any previous chemistry) has been a topic of discussion for years, and while some people see it, again, others may disagree. I've always seen chemistry between the two of them, but I can also understand why it could be argued that they have no chemistry. It's all a matter of opinion.
Janeway and Chakotay just don't work as a couple in my opinion. One of the main problems is probably that Chakotay to me has been little more than a cardboard cut-out character-wise for the majority of the series. Kirsten has remedied that to a certain extent in her previous novels, but it's still hard for me to see what a strong woman like Janeway would see in him.
Chakotay did fade into the background a bit in the later seasons, IMO. Janeway was (and likely always will be) a head-strong woman who goes after what she wants and what she believes to be right. But I agree with Christopher
that Chakotay was much less of "cut-out" in the earlier seasons. I think that's due to the wide range of things that we saw in his character. We saw anger, passion, caring and curiosity. It's a shame that the later seasons didn't showcase as much of that. However, I think that Kirsten has done a great job with his character in the novels.