Captain America and Thor were also not as popular back then outside of comic fans.Marvel was huge in the 60s and 70s. Those guys took a back seat to the X-Men in the late 80s early 90s. But that had to do with the edgier comic stories running at the time (The same kind of stories they lambast Snyder for adapting) and the X-Men cartoon blowing up. This is from the Avengers cartoon that took over after X-Men:
There's a reason Cap, Thor and Iron Man are at the top in this image (Them not being in the show is why it also only lasted like 10 episodes.) Iron Man was always big, it's just that the X-Men were bigger at the time.