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.
Right, and not just for fictional characters. How often do we look at an involved couple that we're acquainted with and think "I don't know what he/she sees in her/him"? Sometimes we can't understand what attracts two people to each other, but that doesn't mean that the universe is writing them out of character. It just means it's subjective.