His journalistic fiction, or fictionalized journalism, has been controversial for a long time. The Bush Administration tried to court him, early on, granting him a ton of access, but that strategem hasn't worked out very well.
If it was just his criticism of the way the war has been handled, I don't think there would be any controversy. Every hack in the Western world has taken his or shots, to one degree or another. Including me. I still don't forgive him, or his war room, for allowing bin Laden to escape from Tora Bora, by trusting Afghani tribesmen to cover the back door. It also seems clear, that we should have had more troops in Iraq from the start, so we could really nail down Baghdad and the Sunni Triangle, not to mention off Sadr and his nutty militia. Putting a few men on the borders might have been a good idea, n'est ce pas? Ew, I spoke Fwench! Gotta go wash my paws.