Gilgamesh in Fate Stay is a person you're supposed to dislike (even despise) in the routes he stars in a main antagonistic role. He succeeds at it because of how he tosses around his overwhelming power, his attitude towards the protagonists, and the way he acts in general. And all of that makes for a great villain.
Which doesn't mean people don't like him as a character. Heck that's the entire point! I like Gil as a character in FSN because he makes a good villain!
I'll admit that Fate/Zero is kind of what made Gil for me as a character, because even though he's manipulative, corrupts Kirei, doesn't give two shits of respect for most people, and flaunts his power and superiority all the time, he's so goddamn amazing at all of it you can't help but cheer for him!
TL;DR: A character can be amazingly likable and great at their role, but you can still dislike them as a person (especially if that's their point).