Kevin identifies one portion of the Newsweek story that's getting consistently overlooked. If Newsweek really was pursuing such a pack of lies, why then, when they ran the story by the Pentagon, didn't the officials flag it as false? They gave them the heads-up, hell, they gave them the text! And yet no one seemed to think the upcoming government report wasn't going to include the Korans-in-toilets factoid. That right there should tell you plenty about why the piece ran.
It's reminiscent of the National Guard memos, wherein the Bush administration clearly figured they were true and declined to challenge them when the story broke. in both cases it seems that the facts were essentially straight, its the sources who were out of line. But you can't fault Newsweek -- they gave the higher-ups the opportunity to correct the error and, if you believe the article caused riots, to preempt those, too. The Pentagon failed.