Alright. I could be completely off-base here, but I've always viewed this song as being about the Civil Rights movement, particularly MLK and or the Native Americans. Bear with me here:

For treated indigenously, digenously
Human right is private blue chip, pry

^ This means that they are being
treated poorly even though they are indigenous to this country (America, this being the Indians)

We're the prophetic generation of bottled water, bottled water
Causing poor populations to die, to die, to die (For treated
indigenously, digenously) (Human right is private blue chip, pry)

^ This is showing that us (Pioneers, whites) view themselves superior, being almost prophetic.

You, you went beyond and you lost it all Why did you go there From
beyond you saw it all why did you

^ This has to do with MLK, it's saying that he was above all the racial segregation, and inequality because of his education and social status but he still went to help those less fortunate (losing it all being his assassination)

We lost consumer confidence in casual karma, casual karma
Confetti, camouflage, camouflage, the flage, the flage
(For treated indigenously, digenously)
(Human right is private blue chip, pry)

^ This line is rather unclear, and is something so deep I wouldn't want to even TRY interpreting it unless under the influence of rather strong hallucinogens.

She lost her mind
Someone kicked her into the back of the line

^ I interpreted this is being about seating in lines, buses, theatres, etc., where the blacks were always pushed to the back.

Dreaming of screaming
Someone kick me out of my mind
I hate these thoughts I can't deny
Dreaming of screaming
Someone kick me out of my mind
I hate these thoughts I can't de--

^ Deep down, the white supremacists know that what they're doing is morally wrong, and they hate all of the prejudiced, biased thoughts that they have, but can't suppress.