The scenes that most people remember are Bart skateboarding naked and Homer having Spider-Pig, each of which happen before the main plot (Springfield having a dome put over it, due to being environmentally unsafe, and the Simpsons escape, due to the residents wanting to execute them after Homer caused it).
Back when the movie was released, it was amongst the highest-grossing movies, so its not like it was some niche movie.
The only reason anyone even remembered this one (past tense because I'm pretty sure it's fading) is because it was in all the trailers and stuff. Everyone knew all about spider-pig before the movie was anywhere near release.