This article from The New Yorker makes, I think, some really excellent points about the outrage surrounding the Rolling Stone cover featuring Dzhokhar Tsarnaev.

Many commenters on Facebook have complained that the image gives Tsarnaev the “rock star” treatment... But these elements are not engineered. What is so troubling about this image, and many of the others that have become available since April, is that Tsarnaev really does look like a rock star...The earliest image, made available by the F.B.I. while Tsarnaev was still the target of a massive manhunt, showed him near the bomb site in a backward white baseball cap. He looked young, and chillingly anonymous, just another dude in a hat, a kind of bro-bomber. Then others surfaced: of him as a baby-faced young man; a shot of him at his high-school graduation, in a black robe with a red carnation pinned near his left shoulder; others of him smirking, smiling; one in which he wears aviator shades—the kinds of digital snapshots that every young American projects into the world. What we didn’t see, and what perhaps we longed to see in our grief, or anger, or confusion, were any familiar images of the Islamic terrorist.

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Emphasis mine, because I think this is the source of so much of this outrage. It's not indignation, it's discomfort—our concept or "what is a terrorist" is challenged. Reza Aslan, a fantastic writer, shrewd scholar, and overall charming dude (whom you have probably seen on The Daily Show) talks about "how to make a terrorist" in his book Beyond Fundamentalism (originally published as How to Win a Cosmic War). I highly recommend it and his other books as well.