Michael Moore is to the left what Limbaugh is to the right. He's the master of the partial truth and the internally-consistent alternate reality. (though some of his most disputed statements in F-9/11 have subsequently been proven correct)
He only got $6 million from F-9/11, despite the film grossing around $150 million. But that's pretty typical Hollywood economics.
When you control the distribution, you can write any deal you want. But when the film is in the can, all a director/producer can do is angle for the best offer.