That, and there's the fact that SOMEBODY gave him up. For all we know, it was the guy three houses down. There's also the fact that, if you lived next door to the Manson family or to Adolph Hitler and knew blow by blow what they had done and/or were capable of, would you confront them directly? The man was basically a psychotic mass murderer. If you were in that village, you best bet was to either lay low or inform the officials...quietly. You don't do something to attract the attention of a guy who gets his kicks by beheading basically random people.
If "the whole village was seized" prior to the airstrike, prolly more than one person told of al-Zarqawi being in that house.