Ty Burr of the Boston Globe writes that the story itself is legitimate, but the cover shot is not. The cover shot was put there to sell magazines and all other considerations were ignored. It's a matter of nuances and choices. From what I've read so far, Rolling Stone, of course, is now using its BS rationalization to justify what it did. Ty Burr in his article says this---
By putting this Tsarnaev on the cover, Rolling Stone at best plays with and at worst buys into the accused’s own manufactured image, casual but potent, speaking in a language we all understand. Worse, by placing his selfie within the context of a magazine cover, a format regularly used to sell rock stars, movie icons, and models, the editors have collaborated with Tsarnaev in the creation of his own celebrity.