I just couldn't watch the episode "The Covenant" and listen to Gul Dukat lecture (now colonel) Kira on how the Prophets have abandoned the people of Bajor without thinking of the chapter "The Grand Inquisitor" from Dostoevsky's "The Brothers Karamazov". Ivan, one of the Karamazov brothers, tells the story of an inquisitor who denies Jesus Christ because he believes that, though God is most definitely real, he has done harm to mankind. He comments that though God wishes men to live not by bread alone, most men are not strong enough to live without bread. The Inquisitor takes the place of God in building a future for mankind and is motivated, not by power, but by altruistic love.
In this way, Dukat may be something like him (although Dukat's intentions are not quite clear at the point I'm at). Kira mentions that she believes he has changed. He longs for the Bajorans to love him for what he did to their planet and people; a longing that will never be satisfied.
So he has allied himself with the Pah-Wraiths against the Prophets, as Nimrod challenged Abraham and the Grand Inquisitor challenged Jesus Christ. Perhaps it is because he believes the universe is unjust and sees the Pah-Wraiths as a source of hope. Perhaps, like the Grand Inquisitor, he is truly motivated by love. Or, more likely, he is motivated, like Nimrod, by his own insatiable lust for power. He would rather all men turn to bricks for him to build his own monument with. It matters little to him, as we saw in the occupation, whether or not their bellies are full