Igor always hated Muggles because he was told to. He never met any, certainly not at Durmstrang, and they remained for him like a plague in another land, distant and foul.
It wasn't until he left school and went to work for the Ministry that he understood firsthand. The Muggles were cruel and simple-minded, the governments that ruled them even more so. Their leaders wanted secrets, Veritaserum, the Killing Curse that left no trace; they built hideous things that cursed thousands at once and stockpiled them like Galleons.
Igor knew Muggles were inferior beings, but more importantly, he knew why.