I know what you mean by "more popular in the 90's," but I don't think it has anything to do directly with literally how many people keep up with the big gray gecko.
In the 90's there was still a movie every year but us folks on the west just weren't seeing most of what was happening. The fan press from the 1990's blossomed out of 1) adults who grew up with Godzilla as kids seeing the monster in new contexts and 2) the fact that at the time Godzilla was not a very strong presence in the west, and his movies didn't get here anywhere near as fast as they did in the 1960's and 1970's.
It was more of, the 90's were when the newer stuff was harder to get any real information on, but with the help of G-Fan, the internet and a generation of older fans who were trying to bring awareness to the western fans, it really turned into this actual community... like the sort of thing Trekkies have and stuff. Except about Godzilla... if you know what I mean.
In the aughts the internet was no longer this big scary thing and information was more readily available to people who didn't have to be superfans to know where to look. That was the era when Rodan's Roost and it's inferior competitors attracted the younger fans (90's kids like me, generally) who took to picking apart movies still in development and such. And it was still a large community, but things were different, because now the gradual release and licensing of goods in the west had sort of saturated, and in the aughts we had finally gotten used to being surrounded by Godzilla merchandise and getting to see the new film not long after it came out, on DVD, with subtitles.
The thing that bugs me is, at around GFW, all the stuff the 90's fans were asking for in the 90's (bring back Anguirus/Gigan/etc., DAM-style movie, more X-ians plz, all the rest) actually happened, and apparently if you give the fans exactly what they want, they will hate you forever. Also, GFW did something else that broke things up. In 1998, just the fact that GINO existed brought the fandom together, because it was, you know, hyperbolic word for bad. After GFW, there suddenly seemed to be "fans" who... liked... Zilla. Disgusting, I know.
Like what Kinggoji was saying, Godzilla's actual popularity is constant. He's Bugs Bunny, Star Wars, Hamlet, he's too much a part of pop culture to worry about not being well known by a large group of people. What's changing is our perception of him. That is to say, when the fan community was the strongest and most like something Trekkies might be, was precisely when you suggested Godzilla was at the height of his popularity.
To be honest, I'm really burned out on fandoms at the moment, and I've avoided the roost and Toho Kingdom like the plague for years now. So, I honestly have no idea what other groups of people are saying about the big gray gecko these days. I'm of course offended that they're making yet another GINO (although I heard Toho was going to insist on a practical Godzilla, I could never find a source, and looking for news about that movie is depressing), and a part of me up and decided Guilala was the new king of the monsters a couple of years ago.
But, as far as I know, Godzilla is still as popular (and lucrative) as ever, it's just that G-Fans are too varied a group now, and it doesn't seem as cohesive as before. But there's plenty of them. Apparently a bunch are comic book fans as well.
I've always said that./