There could be quite a few things.
1. Over-sensitivity. On one occasion I put up a post with several reasons why Chakotay would have made a better captain. Someone immediately accused me of hating women. I don't hate women, and I actually really like Janeway, middle school principal voice and all. Critiquing Janeway is not hating her.
2. Disliked decisions. These include but are not limited to stranding her crew in the first place, splitting Tuvix, making deals with the Borg, going nuts with the Equinox, obliterating the timeline in Endgame, and refusing to promote Harry Kim.
3. Backlash from the "Janeway is awesome" trope. There's a reason why I call Janeway the Chuck Norris of Star Trek, and it's not fully complimentary.
4. Her series has not aged well. DS9 was the bastard middle child when it was in production, but now it's considered one of the best Treks ever. Voyager, contrastingly, fell far short of its potential. This is largely because of a conscious decision to back away from the show's unique aspects (deprivation, lack of support, and potential internal conflict) and turn it into TNG Mark II.
5. Unfavorable comparison to DS9. Did you see a neglected character on DS9? I didn't. Compare the incredible development of Sisko against the relatively static Janeway, Kira against Chakotay, Nog against Kim. And unlike any other second-wave (1987-2005) Trek, I can't think of one character who wasn't promoted appropriately.
6. Sexism. As deplorable as we might find it, it's a very real thing. Would the 2016 Ghostbusters reboot have gotten as much hate with a mixed cast? I doubt it.