Ok, as Hazeldountlovesbullet, I didn't post meanings for this song for some reason. I'm explaining the American Idiot Musical song by song, though, and the meaning is pretty much the same.
In the musical, She's a Rebel is combined with Last of the American Girls, right after Give Me Novacaine. This is my personal favorite on the soundtrack because it is sung by both Johnny and Jimmy - which is odd because its like listening to him argue with himself, because Jimmy is a really just a part of Johnny.
Johnny is in love with Whatsername and sings Last of the American Girls as praise, but Jimmy cuts in with She's a Rebel, giving the song a negative connotation as he constantly repeats "She's a rebel and she's dangerous!". Whatsername is everything Johnny ever wanted, but Jimmy for whatever reason, doesn't seem to want them together.
The next song is Last Night On Earth.