I know She's a Rebel is probably the most-hated song on American Idiot, but I like it and it fits the story. If you think about it, it's the only happy moment throughout the whole story. Jesus/St. Jimmy is happy for a brief time, while he and Whatshername first get together. In the the next song, he feels like dying, she is sick of crying - things start going bad. So I think, while it's not the greatest song in world, it serves the story well, and gives the characters at least a bit of hope in the midst of pain and heartbreak. On an interesting note, the song is also sort of about the statue of liberty.