Misguided
Technically, this film is adept. The concept behind it is where the trouble lies.
What happened at Columbine was tragic, there is no argument. And while I consider myself a leftist, I refuse to give sympathy to sociopaths. I had a shitty high school life too. I was picked on and had the shit kicked out of me and called every name in the book. But I didn't pick up a gun and hold target practice at lunch hour, and neither did the thousands, if not millions, who can sympathize.
So why do kids bring guns to school and take their revenge that way? Maybe because stuff like this, or Gus Van Sant's Elephant. While I thought the film was exceptional and this flash (at least in terms of construction, animation et al) was well done, both make the mistake of glamorizing/exemplifying Eric and Dylan as tragic martyrs of a society that had no room for them, and that's precisely the message to give if you want this to happen again.
I guess if I have to shrink my thoughts to a sentence or two, it would be this: life is hard for everyone, and most of the time it stays that way. But the truly strong are the ones who survive. Those who bring guns to school for their "revenge" are merely cowards, not heroes or martyrs, and there is no beauty in their plight. Just the ugly truth of what they are: murderers.