The fans don't hate Charlie, they just wish he would give the other characters the spotlight.
Charlie isn't hated by the fandom but is frowned upon by them.
The viewers may hate Charlie's guts, but the show feels somewhat empty without him there.
The writer is trying to help restore the character from derailment, but has not quite gone the way about it.
Charlie is the writer's idea of a good character, however he is constantly trying to shift it after his dislike from the crowd. The reason he always appears is because they keep trying to put the character in a light that works, but due to fan dislike of the character he's still considered annoying, even if his role for the episode was actually good.
Conversed: "Oh, man, not this guy again..". "Who, Charlie?" "Yeah, him. He's taking over the show, and it's really hurting the quality".
Deconstructed: Charlie, a character in a Show Within a Show exists within the writer's blind spot because he's what the author always wanted to be: confident, outgoing, witty, with lots of friends... the writer put so much of himself into Charlie that he doesn't want to acknowledge the character's Hatedom, as it strikes a little too close to home. So when the fans are torturing and murdering Charlie in Flash animations on the in-universe equivalent of Newgrounds, the writer sinks into depression and takes his own life.
Reconstructed: Charlie from the Show Within a Show isn't the author's idealized self image, as much of a Marty Stu as he may be. Rather, he's what the writer thinks all of humanity should live up to, and thus doesn't sink into a depression when the fans hate Charlie but rather treats it as the fans being intimidated by how great he is. They crucified Jesus, you know.
Plotted A Good Waste:
Turns out the writer was just settling Charlie up for a major fall in a Wham Episode where all his faults come to the forefront and have disastrous consequences, causing him to lose his friends' respect and setting him up as The Atoner.
Charlie is deliberately written to be annoying...so the audience will root against him when he betrays the team.
Played For Laughs: Charlie is set up by the other characters as over-the-top perfect so that when he fails (Once an Episode or more), we laugh at the disconnect between his public acclaim and how he actually sucks.