As both a born-and-raised Bostonian and a graduate of BU who once had an on-campus apartment in Kenmore Square not at all far from the bomb location, I had no problem with the cover. It seems absolutely appropriate for the story they are running, which deserves (at least in concept, not execution - I've yet to read it) to be explored for the reasons Henrik put very well.
I also believe they could and should write an excellent piece about the first responders and survivors whose stories are all extremely worthy of recounting. But I in no way believe that the cover of a magazine is in any way an endorsement or glamorization. It is an accurate depiction of the story this issue tells.
I haven't bought an issue of Rolling Stone in years, or any magazine for that matter (I happen to like RS more than the average mag, actually). It did make me curious, though; they do have a very well-earned reputation for hard journalism and longform writing that non-attentive readers might be surprised by. I wonder, how often have any of Matt Taibbi's exemplary works been the cover art and not just a mention on the cover?
Words don't deserve that kind of malarkey. They're innocent, neutral, precise, standing for this, describing that, meaning the other, so if you look after them you can build bridges across incomprehension and chaos. But when they get their corners knocked off, they're no good anymore…I don't think writers are sacred, but words are. They deserve respect. If you get the right ones in the right order, you can nudge the world a little.