Less antichristian and more anti organised religion in general, saying to focus less on blind dogmas and think critically. The reason why Christianity was chosen was due to its prevalence in the western world. Had something like Hinduism been chosen, the message would not have been as clear.
When there are depictions of Christ, he himself isn't made fun of, the very beginning of The film being a good example, when giving the sermon on the mount he is shown as one might expect on your sunday TV. The true ridicule is aimed at those trying to hear and failing in general since they and we are sinners and always fall short.
The main issue as to WHY its an issue in the first place is because the constant misunderstanding that it's a personal attack.
Aside from that, its a little long but still a good film.