I think people are confused because the movie itself is not just Alice in Wonderland it mostly is Through the Looking Glass which is the sequel to Alice's Adventures in Wonderland. I think if your familiar with both books you'll really enjoy the movie, if you're only familiar with the Disney-fied version then you'll just be confused.
I loved the movie. I thought it was a very Tim Burton movie. It was so funny to me. The humor was really in the dialogue. If you can't follow the dialogue then the humor is not there.