Nietzsche never characterized himself specifically as an atheist, and although he came from a very religious background, descended from several generations of Lutheran preachers, he never understood the Bible or Jesus. He also started out his education studying to be in the clergy, but preferred to study other things eventually.
In his writings, Nietzsche had the highest praise for Jesus Christ, and admired him openly, although he severely criticized every other thing that he ever discussed in his printed works. He is famous for having said "God is dead, and it is we who have killed him", and this perfectly summarizes Nietzsche's understanding of religion as it existed within Europe in the 19th century. He knew about and admired Jesus Christ. He knew that Christ had died. But he did not understand about the resurrection. When Nietzsche discusses Paul, he has only criticisms of him and despises him terribly.
Since he didn't believe or understand about the resurrection, obviously he thought Paul was a nut job.