My problem with Conner isn't so much that he hates Angel, it's that he's hateful and mean to every single member AtS (except Cordelia and I think his kindness to her stems from less than selfless intentions) even after these people showed him kindness and genuine concern for months. This constant attitude of "me against the world" when he has Fred, Gunn, Wesley, Lorne, Cordelia, Angel even Faith for a short period treating him like family makes him extremely unlikable.
I could understand his "lone wolf" attitude if he were alone like Wesley was for a while or Lindsey, Faith etc, but he continues to accept everyone's hospitality and unconditional love, patience and forgiveness while treating them all like they are unintelligent enemies.
I'm not even getting into the fact that he helped murder an innocent against the pleading of his mother and attempted to murder Cordelia and many others in the bomb scare.
To me, Conner is the single most unlikable, unforgivable character in the Whedonverse. I agree that Season 5 Conner is likable but I'm not sure I can trust that Conner since I know that all it took was a rough breaks for him to turn into a raging, murderous, whiny psychopath. Wesley, Liam/Angel, Fred, Faith, Lorne (most everyone) went through horrible tribulation and they didn't all turn into psychos (Faith did but she genuinely repented something Conner never does).
This Willow quote from Choices pretty much sums up how I feel about him "It's way too late. You know, it didn't have to be this way. But you made your choice. I know you had a tough life. I know that some people think you had a lot of bad breaks. Well, boo hoo! Poor you. You know, you had a lot more in your life than some people. I mean, you had friends in your life like Buffy. Now you have no one. You were a Slayer and now you're nothing. You're just a big selfish, worthless waste."
Sorry to all the Conner fans I've offended, I just finished rewatching Angel Season 4 and I'm always really riled up against Conner after viewing it.