I never used to understand it either. I think part of it is how different it is from the rest of Dookie. Most of Dookie sounds like its album cover, if that makes sense--bright, dry, kinda washed-out, like a really hot summer day. And the music videos for the other singles tend to reflect that, they've been chemically altered to wash the frame out and there's a very harsh brightness to them. Whereas WICA sounds like the accompaniment to wandering down a city street at night, which, again, its video reflects. It's such a different mood from the rest of the album, which really makes it stand out as memorable.
There's also the fact that it's easily the most recognizable guitar riff on Dookie. Basket Case has the most recognizable melody overall and Longview has the most iconic bassline, but in terms of guitar WICA is the standout.