Well, there are a LOT of people in this fandom, so there are a lot of varied opinions about that baby.
But if we’re talking about the specific subset who both hope Mary will die and want Sherlock and John to raise a baby together, I can see two reasons for it, and there are probably people who hold to each.
The first is that some people have a highly developed grasp of the difference between what they want out of their canon and what they enjoy in a fanfiction story. They are two very different contexts, after all, and I think that these people are right that what might work for one would not necessarily work for the other. For example, while they might adore fanfics where Sherlock raises a baby, they may have a keen sense that the show is much more grounded in the film noir detective genre, with a lot of focus on adventure and characters who are edgy and kind of fucked up. Definitely not the place for baby stories.
The other reason is that some of them have a very strong loyalty to the idea of Sherlock/John, and resent Mary and her baby for intruding on the relationship that they are invested in.
My own concern about the baby is just that thematically I don’t see how they can make the show work with a baby on board. But I also figure that they spend a lot of time, effort, and money on this show, and they’re not going to suddenly declare that it’s a domestic sitcom, so either they’ve got other plans for the kiddo or else they have thought of something I haven’t.
Although of course the problem with Moffat in particular is that he frequently thinks he’s got the best idea in the world, but it turns out to really be a terrible idea. So I guess there are actually three possible reasons. The third is that for a lot of people, what looks like hatred and panic about Mary and her baby is really just Mary serving as a touchstone for their real fear that Moffat may Moffat this show off the rails in the coming seasons.