Quite simply, with little explanation, this song can directly relate to the current "struggle for god" if you will.

Angels=secular population

Father=god obviously

Monkeys=the "other" people

1st verse, the key words are "puzzled and amused, free will, holy garden,..."
-this could be an islamic view of christianity. Too free spirited, free minded, free in general. However they stay amused rather than spitefull or opressive. Also, a view that western civ. is greedy and all-obsorbing of the earth.

2nd verse, the keys are "baffled and confused, reason, monkey killin monkey..."
-a western view of the middle east and islam. Not amused rather confused, takenaback if you will, a bit more eager to meddle. Seeing others as unreasonable, lesser beings, engaged in ferocious territorial warfare.

3rd verse, keys are the fact that angles are left out, and it starts right in with "monkey killin monkey, beat their brother, repugnant is the creature.." -I see this as TOOLs view of the whole sit. you're both monkeys, we're all brothers, all of us are simpley killin over peices of the ground, "cuting it all right in two!"

Finally, all the angles are benched, the sec population is left inept as they wait for this tug of war to end, in the end the "common people", on both sides, are the angles that are pushed aside and are left baffled, confused, puzzled, and unamused... i m o...

Peace.