From the available reports on the incident, it seems clear that the U.S. knew exactly where he was, and had plenty of troops surrounding the building before they called in an airstrike and dropped (depending on the story) one or two 500-1b. bombs directly on him.
It seems like they really wanted to kill him, not capture him. There is even a witness report that when they discovered he was not dead, his US captors beat him and made sure he died of his "wounds." Whether or not that report is correct, the bombing itself was certainly meant to kill him.
Now that's mighty curious when you think about it (which not many in the mainstream media are bothering to do).
I remember thinking, and writing, the same thing when the U.S., early in this occupation, had Saddam Husseins two sons trapped in a building and, instead of waiting them out and capturing them, with all the information they surely had about the whereabouts of the old man and of the organization of the Baathist resistance, the military blew up their house with rockets and bombs.
In Zarqawi's case, killing him with bombs meant, incidentally, the killing of an innocent little girl, aged 5-7 according to reports, and her mother and father. It could be that her parents were not so innocent (in which case sais la non vie), though we don't know that--they may have been pressured into letting him stay in their home--but the little girl who died to satisfy Americas bloodlust was an innocent.
Remember, this was done on orders of an administration that claims to believe every life is precious.
So let's get this straight: there was no justification for bombing that house. The U.S. military had Zarqawi in a perfect trap. He was surrounded. There was nowhere to run. There was a predator drone monitoring the site from above in case he tried to slip away.
So why did they kill him?
My guess is that it's the same reason they killed Saddam's two sons: The U.S. is not particularly anxious to have these guys talking about what they know about the U.S. in Iraq.
In the Saddam boys' case, they might have told tales of U.S. assistance to their father. At a minimum, they might have made it clear that there were no weapons of mass destruction, and at the point they were caught, the administration was still funding a desperate search to find anything (there is even talk that they may have been considering hiding something so they could find it).
In Zarqawi's case, there is speculation that he was something of an American creation. Certainly the U.S. left him alone before the war and during the war's early stages, when he and his gang or terrorist thugs were operating out of northern Iraq under the protection of the U.S. no-fly zone.
At the least, we can say that the Pentagon and the administration (because the decision about how to handle Zarqawi was surely made at the very top by The Decider and his advisers) made a stupid decision in killing him, rather than capturing him. If we think more suspiciously, there may have been method to the administrations madness.
They don't want these kinds of guys talking about what they know.
And for that, a little girl paid the price.