You can quite plainly see a difference in the internet "culture" or however you call it between the start and now. Sure, people were more "-phobic" but also you like, didn't have to interact with those people. They were in their separate area and you were in yours, with your people who actually, were gay and trans and made all the lovely weird fanfic and had fun. Instead of being stuffed into one big fat Twitter. You know like, you would have one forum with those guys and another forum with your guys. It was just common sense to keep to yourself and foster your community. Also, obviously the internet being homophobic and transphobic was a microcosm of (English-speaking) society at the time. Much like media! This is not news, to me...
And even then, did we have these people calling the fujoshi actual rapists or pedophiles over their yaoi ships? As far as I can tell that's something that emerged more in the last decade. I'm sure it happened occasionally, but not to the scale of now. As an example (from personal experience/memory so take with a grain of salt), there was a deviantArt group for incest ships, and another one against incest ships. The latter basically just talked about how much they didn't like those ships, but they didn't go out and harass the people who did. And the former said to just ignore what the latter group did.
Also, I think that the age range of internet users skewed older in the past? But I'm not too sure since there also use to be more websites catered specifically for kids, like MMOs. Which was another advantage, there were more places like this, and in having those websites there was also more of a push for teaching internet safety consistently. I remember things like not sharing personal info being drilled in, which I can't say is as common now because lots of younger people post identifying info too readily. Though unfortunately children were targeted by predators on these websites and MMOs... It's a lot to unpack.
I think the big thing is that the older internet didn't feel as corporatized as it does now. There was always that sense of it, as companies always had websites and ads. But again, it didn't feel as in your face. If you didn't want to see it, you just didn't go there. Even the couple of bigger websites that were run by corps didn't have all the same "isms" they do now. YouTube of 2008 is not run the same as YouTube of 2025. Neither deviantArt, or... uh, what else was around then? Lol
Well, I think another big thing that separates new and old internet was the way you found things. You had to have a bit more ingenuity, more determination, maybe, to find your niches. And that made the internet as a whole feel more exciting; you never knew what you would find, and your woeld would become more open. This is very much a double edged sword. Because you can find truely beautiful and genuinely horrifying things. And it probably also contributed to the whole "-phobic" thing, like lots of straight white men who have only ever traveled 50 miles from their hometown being unable to comprehend the idea of a furry. But again the other edge is the closeted trans lesbian finding out that there are other people that feel that feel the same way.
Well, the main takeaway I get is that the web is a very complex and changing invention, and we have all changed with it. I do personally think the older web was "better", with aestericks, and I would take its caveats over the ones of today.