Just because part of an apology is to make the person apologizing feel better doesn't mean that it's not honest. If Karofsky wasn't sorry for what he did he wouldn't have needed to feel better by apologizing, would he?
It's also incredibly hard to change ones self when you're afraid that by doing so you're going to be persecuted. Keep in mind he only became a member of the bully whips because Santana threatened him. Karofsky is scared to come out of the closet. It's a big thing to ask someone to change when they're not ready, like when Kurt told Karofsky to come out of the closet. It's irrational for you to expect him to change on his own will, not when his life is controled by the fear of persecution by his peers.
Re: Spoilers for Prom episode
It's also incredibly hard to change ones self when you're afraid that by doing so you're going to be persecuted. Keep in mind he only became a member of the bully whips because Santana threatened him. Karofsky is scared to come out of the closet. It's a big thing to ask someone to change when they're not ready, like when Kurt told Karofsky to come out of the closet. It's irrational for you to expect him to change on his own will, not when his life is controled by the fear of persecution by his peers.