Bush's speech noted:
"We have difficult work to do in Iraq. We are bringing order to parts of that country that remain dangerous."
"Our mission continues...The War on Terror continues, yet it is not endless. We do not know the day of final victory, but we have seen the turning of the tide."
The speech also said that:
"In the Battle of Iraq, the United States and our allies have prevailed."
From the cited article.
"Major Combat Operations" were over. The guerrilla insurgency was stronger than expected to be sure, but there's a big difference between that and the kind of heavy combat that the crew of that aircraft carrier were there to perform.
The decision doesn't have to be logical; it was unanimous.