Honestly, I have never been upset about Dukat's usage in Seasons six and seven. Ultimately, Dukat was a character about choices - what we saw in seasons four and five had shown us that if he'd chosen to be, he could have been a good man. However, he instead saw the chance to gain power, to force the galaxy to accept his view of himself - as a god among men. He may not have seen himself as the villain, but he certainly had a superiority complex - he was BETTER than the Bajorans, the Federation... even his own people. He did engage in secret negotiations with the Dominion and got himself made head of the Cardassian government, after all. And Dukat always saw Sisko as the closest thing he had to a rival. So it makes sense that, once he begins to realize that Sisko is so important to the Prophets, as they dealt with the Dominion reinforcements in the wormhole, he certainly couldn't let someone else be better than him, so he sought out the Pai-Wraths.
Dukat may or may not be the most evil man in the galaxy, but he's certainly the most reviled Cardassian on Bajor. If he really did do such altruistic things for the Bajoran people, why exactly do they hate him?