Everyone's entitled to change their mind. Burton could have initially liked the movie but changed on reflection.
Also Burton is an actor and he could have been playing for his audience. It probably never hurts to say positive things about Gene at a Star Trek convention. And if the audience were chiefly 24th century Star Trek fans then maybe he thought he would share his movie misgivings with them.
Frakes also shared some misgivings about ST09 when I saw him at a Convention. None of it was really all that bad. He's entitled to his opinion and like his movies better. He should.