"It seems to me I heard our Commander in Chief declare the war over not too long ago."

No, the war in Iraq continues, the Commander in Cheif did not state the war was over.
I think it's fair, to apply international law as though the war was over- we must follow what's required of a occuping power.
But Iraq is somewhat unusual in that previous leadership is behaving as though they were criminals, and we are still hunting them down like criminals. In other words the Iraqi regime has shattered, they no longer an organized unit in which they have the capability to "end the war"- surrender.
So, the situation is similar to entering country in which the leadership has vanished and we are maintaining order with our soldiers, until such time as we can form a government.

"We are rapidly squandering what good will we had."

This is only true in the rather confused dreams of the Left.
First they couldn't admit there was any good will, now they have moved on, to the say we losing it.

"Yes, the American people are responsible. All of us. To suggest that those who oppose the war sit down and shut up is to suggest turning off political dialog."

Look there isn't "much" dialog in, "We hate Bush". True, the Left can discuss their feelings about how much they hate Bush, endlessly. But it's not very important in terms of national issues. Now, I don't believe said anything about shutting up. But, yes, to the hecklers, I would say "Shut up!". But to people who have real information, or people who drawing conclusions from real information, of course, we want dialog.