Yeah, they do

Now the right is after Isikoff and Newsweek over an apparently inadequately confirmed story that a U.S. military investigation had uncovered evidence that Americans desecrated the Quran while interrogating Muslim prisoners at Guantánamo Bay. The disproportionate firestorm over Newsweek's stumble has less to do with the riots the story sparked in the Muslim world than with the riotous power of Republican bullies and their allies in the White House and the right-wing blogosphere. It's absurd for rightist blowhards to try to paint Clinton-critic Isikoff and his editors as part of a vast left-wing conspiracy determined to undermine our troops in Iraq. And they need to be called on their intimidation campaign.

— from Salon's Newsweek isn't the problem

The Salon article is, I'd say, a pretty good summary of the situation. Fact is, the story here isn't one slightly shakily researched piece (whose substance, from other reports, actually isn't that startling, and probably quite accurate). The story is systematic prisoner abuse and the administration's efforts to intimidate anyone covering it.

See also, in Newsweek was right, from The Nation via Yahoo:

Contrary to White House spin, the allegations of religious desecration at Guantanamo such as those described by Newsweek on 9 May 2005 are common among ex-prisoners and have been widely reported outside the United States. Several former detainees at the Guantanamo and Bagram airbase prisons have reported instances of their handlers sitting or standing on the Koran, throwing or kicking it in toilets, and urinating on it.

— from Newsweek was right in The Nation

So yeah, the facts reported are, probably, essentially correct. And as per Salon, the blowhards do need to be called on this.