Amadeus. The main character is Savaleri, not Mozart.
Rosemary’s Baby. The main character is Rosemary. The baby is never seen.
People have argued the main character in Jesus Christ Superstar is Judas.
Salieri
Charlotte’s Web–the main character is Wilbur, not Charlotte.
Harvey–Elwood P. Dowd is the main character.
Oh, thought of another one. Rain Man–the movie’s really more about Charlie (Tom Cruise) than Rain Man/Raymond.
Yeah, your right.
I still hold the belief that it was a bad movie though. You aren’t going to make me change my mind about that! No matter how much you try! 
That’s what I thought, gotta rent that movie again.
I got the e-mail on this before the edit. Whew!
Forgetting Sarah Marshall
OH! The Rocky Horror Picture Show!!
It’s not really about Savaleri, either. 
And it is very much about Mozart, but as seen through another character’s eyes.
Dracula’s more about the mortal cast than Dracula, really (although he has much more screen time and background in the Coppola version)
Arguably, Dances With Wolves is more about Native Americans and the frontier itself than Costner’s character.
Waking Ned Devine
Being John Malkovich
Garbo Speaks
City Slickers II: The Legend of Curly’s Gold
The main character in The Godfather is Michael.
…who, by film’s end, is the Godfather.
Dr. No and Octopussy
I was trying to think of some TV shows. Will & Grace might better have been called Karen & Jack, who were much funnier to watch.