A.I.
I can’t get sympathetic for a robot child any more than I have sympathy for a toaster oven.
The supporting cast, too… his creator, his “adopted” mom and dad, are all just loathsome, delusional, sick, twisted people. For me, this is one of the worst movies I’ve seen in the last 10 years… and I watch a lot of movies.
I saw a couple months ago, but for the life of me I can’t remember the name of it. It was about a white teenage girl who had run away from home, was living on the streets and was a drug addict. A black woman who took photos of the unfortunate on the streets(and paid them for their photos) came across her after she had OD’d(and her boyfriend had dragged her body outside his apartment). The photographer takes her in and tries to get her to clean up, but eventually the girl just reverts to her old ways, betrays and steals from her benefactor(thus destroying her livelyhood).
I felt the girl was incredibly unlikable and unsympathic, only gaining a little sympathy at the end when she decided to go home(and presumably, get clean). It was so bad that when girl OD’d, I actually suggested dragging her out of the apartment and leaving her on the doorstep, just before the character in the movie did so.
Barry Lyndon in Barry Lyndon.
Although I guess he’d fall under the “Kubrick character” clause already mentioned. 
…All the characters in “Rules of Attraction” and “Kids”
Terrible movies.
Since A.I. was Spielberg’s joint project with Kubrick, the cast the likely falls under the aforementioned “Kubrick character” clause (and I disagree with you about the character of David’s “adopted” mom being).
If you really want to talk about films with unlikeable protagonists, try most of Scorsese’s movies (e.g., Raging Bull, Goodfellas, and** Casino**). I still generally like his movies, though.
Jeremy Irons’ characters, Beverly and Elliot Mantle, in Dead Ringers. Irons pulls off the most amazing acting feat I’ve ever seen on screen. He’s utterly chilling, playing demented twins who are so alike their shared girlfriends never know they’ve been passed around, yet so different that you never wonder which one you’re seeing in any scene. It’s an awesome movie, but you won’t like either character (and it’s a David Cronenberg film, so prepare for extreme gore).
In contrast, I loathed the lead characters in Rope so much, that it made me despise the movie, in spite of any cinematic excellence it might possess.
The female lead in that forgettable romantic comedy Hitch. About the time she torpedoed the male lead’s livelihood, I’d have shown her the door and never looked back.
Oh, and both of the assholes in The War of the Roses.
Troy. Achilles.
The butchering of the myth was bad enough, but the reason I walked out of the film was that I couldn’t stand to watch Achilles any more.
Are you asking about protagonists who were supposed to be unlikable, or ones that weren’t supposed to be, but were.
In the former category:
Aguirre in Aguirre, the Wrath of God. Everybody else was an asshole, to, but he sticks out.
Everybody in Dangerous Liaisons.
In the latter, I’ll second Napoleon Dynamite, since I guess I was supposed to like him.
So far, outside of X-Men, I’ve had a real problem with all the heroes in movies based on Marvel comic books. And in X-men, I like Magneto better than any of the protagonists.
I hate to bring up Tom Cruise again, but I thought his character in Vanilla Sky was particularly unlikable.
Hud.
I didn’t like any of the characters in Saw or Magnolia
All 3 of the leads in The Grifters are totally unlikable.
Anything that sukt in A.I. I blame on Spielberg. He was the director, it’s his baby. All blame or praise, as the saying goes.
I thought all the characters in Ferris Buehler’s Day Off were irritating and unlikeable. Not fun.
I thought all the characters in Alien vs. Predator deserved to hunted/eaten/implanted. Especially those humans who cluttered up the movie.
No one’s said Anakin Skywalker from AotC yet?
Ok. Martin in Martin 
As much as like John Cusack, I hated his character in High Fidelity. He was a self asorbed, snotty, narcicistic jerk.
Come to think about it, he was nearly the same in Pushing Tin.
I had a feeling someone was going to say that. If you didn’t, I would have.