Hermione's crusade is portrayed as comically misguided because it kind of is comically misguided, but perhaps not for the reasons you think. Rowling commented on this in a 2000 interview with CBC Newsworld:
JK: My sister and I both, we were that kind of teenager. (Dripping with drama) We were that kind of, 'I'm the only one who really feels these injustices. No one else understands the way I feel.' I think a lot of teenagers go through that.
E[van Solomon]: In Britain they call it 'Right On' or something.
JK: Exactly. Well, she's fun to write because Hermione, with the best of intentions, becomes quite self-righteous. My heart is entirely with her as she goes through this. She develops her political conscience. My heart is completely with her. But my brain tells me, which is a growing-up thing, that in fact she blunders towards the very people she's trying to help. She offends them. She's not very sensitive to their…
E: She's somewhat condescending to the elves who don't have rights.
JK: She thinks it's so easy. It's part of what I was saying before about the growing process, of realizing you don't have quite as much power as you think you might have and having to accept that. Then you learn that it's hard work to change things and that it doesn't happen overnight. Hermione thinks she's going to lead them to glorious rebellion in one afternoon and then finds out the reality is very different
Hermione is the stereotype of a teenager who sees injustice in the world, and wants to fix it (which is a good thing), but goes about it in ways that are self-righteous, self-involved, and not really helpful.
I would argue that the in-universe response, then, mostly falls into three camps:
- The House-elves themselves, who are being condescended to and understandably don't appreciate it1
- Characters like Ron, who don't see the problem because they've grown up in a system that benefits them. This reaction is most likely intended to make you feel uncomfortable, because it's kind of the stock response to a lot of real-world social issues
- Characters like Hagrid, who know that Hermione is going about her crusade with the wrong attitude; the sensible adult, in other words.
I couldn't begin to speculate on why this subplot was less prominent in later books2, but I suspect it was mainly for character development reasons; Hermione realizes that she's not helping, so she dials back her over-the-top efforts. And then, of course, after Goblet of Fire there are many more immediate issues at hand.
1 Though there's also likely an element of internalized oppression, but I'm far from qualified to talk about that
2 Although I can speculate on why it was dropped from the film; lots of subplots were dropped from the film, because it's not easy to turn six hundred pages of book into two hours of movie