I think that it worked well. Even though there wasn't a romance between her and any (certain) members of her crew, there was still a lot of tension between Janeway and Chakotay, which kept us all asking "Will they...?" for years.
Sure, it would have been nice for there to have been a greater acknowledgement of the attraction between those two characters, but I can respect the decision not to, because it showed the other great aspects of Janeway's character. We saw what a great leader Janeway was as well as her intelligence when it came to strategy.