I was surprised to learn about the hate when I first started watching. I do think some of it is due to sexism. I'm betting a lot of male viewers weren't ready for a woman in the captain's chair.....
Personally speaking, that wasn't the case for me. Gender or Race regarding the Captain was never an issue for me.
In saying that, Janeway did rub me the wrong way many times. Granted, I did like her no-nonsense attitude most of the time, but the thing that bothered me was she seemed to have a more "Black and White" mentality on many situations and there was hardly ever any grey areas with her.
Some people like that, I don't.
For me, it seemed as though she would tell the crew what the situation was, state her position on the matter, then sometimes she would ask the crew for some feedback, but then still stick to her position regardless, as if she already knew every possible angle and outcome and she just asks for their opinions out of courtesy. Many times, Kirk, Picard and Sisko, despite all of them being very clever and intelligent, would get feedback from one particular crewmember that makes them realize something they didn't consider and they would then adjust their position slightly.
Janeway always seemed to know everything already, a crewmember would point out something not yet mentioned and then she would finish explaining their argument almost perfectly, states she already thought about that, dictate the problem with their point they were trying to make and then repeat her original plan.
There were also some instances where her decisions were almost entirely based on her personal morals and would stick by them even when the decision affected someone else more and thus, should have decided what was in the best interests for that person or persons, rather than holding so rigidly to what she thought was right and wrong.
There were a few situations where she eventually changed her position but it was usually after she fought tooth and nail until she realized that what she was doing was not the right thing and could no longer defend her position.
This wasn't all the time, but it was often enough.
Janeway could have been a male captain, an Asian captain or anything else and it wouldn't matter to me. It's about personality and hers rubbed me the wrong way often.
Other captains in the other series'ez, including Enterprise, all seemed to be able to think of the overall picture and understand and take into consideration the views of those around them, but Janeway was just too often jumping to snap decisions. "This is the problem we face, this is what we will do because it is by the book and the right thing to do. Thank you for your input, but the original plan still stands."
Again, I'm not trying to say this was all the time. There were instances where she did listen to everybody, thought about the choices and made the choices that seemed to suit everybody's consideration..... But the times where practically everybody didn't approve of her decision and when her 1st and 2nd officers tried to do their job and point out possible mistakes on her part, all hell broke loose and she'd stop the whole thing with "I'm the Captain, those are my orders."
And it's true, she was the Captain and she had the final say..... But the whole relationship between her and the crew in such matters seemed to have a hell of a lot more friction going on than other crews in the other shows.
Maybe this was done on purpose by the makers of the show to overcompensate any questions of having a female captain by some viewers & thus, show that she had the gusto like the male captains did.... But it just seemed a bit over done.... As if to say that if she changed her view on something too often and didn't stick to her guns, viewers would think she was "weak" which would be far from the truth.
The other possibility in her character being like this is for the ability to show that she is just as flawed as anybody else as you do get to see the consequences of her rigidity unfold later down the road.