>seems like such a stupid fear
Absolutely, but it was a different time back then. Today you have characters like Ramsay Bolton or Negan being everybody's darling, and both of them are ten times worse than Dukat.
But Behr is on recording stating, that after the Marquis two-parter in S2, they didn't want Dukat to become "the friendly neighbourhood Cardassian" and they wanted to make clear that he's "evil". Hence the abusive relationship between Marc Alaimo's characterisation and the writers started to unfold, where they on one hand needed him to carry the main arc, on the other hand felt deeply uncomfortable with him becoming a fan favourite and a scene-stealer. In the end the writers decided to make him an insane villian, and I believe this could have been handled much better.
The fact about him being a two-faced rat is one of his obvious flaws, but it was mixed until the very end because he'd always given platforms to argue his viewpoint even if you disagree with it, yet it came over as sensible. This is why people still talk about someone in 2019 who was basically a side character - if an ISIS fighter tells you he enslaved women and children because Allah told him to, you clearly think he's just nuts, but for some reason Dukat's position is always somewhat reasonable, even if he is a fascist turncloak resembling a tinpot dictator installed by the US in Africa or Latin America.