One of the meanings I think you can find in this song is "Mary" as a personification of the earth itself. It's easy to see:
"butterflies don't belong in nets" (you can't own earth, no matter how hard you try)
the idea of people having destroyed this woman who personifies the earth, having prostituted her (used up her resources), but people are starting to notice. people are starting to want to help - they're "waking up".
the very obvious verse that includes the line "What'll we do when our babies scream? / Fill their mouths with some acid rain?"
One of the meanings I think you can find in this song is "Mary" as a personification of the earth itself. It's easy to see: