The final scenes which show the end of the world and the apocalypse and the passing of all the biblical prophecies (the four horsemen, the trumpets etc) are NOT hallucinatory. They are supposed to be real not inside the main character's head.
Look at the way they are depicted, she is in a police station, and the people around her react to these things, another woman prisoner begins singing "hark the herald angel", the bars fall magically off the cell doors, the TV that is on starts showing the 4 horsemen and angelic figures, and we hear the sound of the trumpet and see everyone: the sheriffs, the prisoners reacting to this.
The point of the film is this: that religious fanaticism may be frightening. But what would be EVEN MORE frightening: what if the religious zealots depicted in the film, what if they turned out not to be misguided or wrong in their beliefs but to be RIGHT: that the Book of Revelations actually WILL come true! This is what makes the film so terrifying.
The very final scene where the 2 remaining characters, Will Patton and Mimi Rogers are in Heaven, shows that in the end even though the world has ended and the coming of the Apocalypse has passed, and the Second Reign of Heaven has come, that in the end, the Mimi Rogers character finally realizes that in spite of her previous choices, that she decides human free will and the right to question, to choose (i.e. free speech) must be paramount, EVEN if this means she is condemned to purgatory forever.
So she chooses NOT to embrace God, this is why Will Patton suddenly vanishes, he chooses to and goes to Heaven, but she allows her earlier doubts, about how God can allow evil and suffering, to prevent her from accepting God as the Saviour. She accepts He exists, but will not follow Him.
So THIS is the film's ultimate message: that human freewill may triumph even against the strongest powers.
I know this may be hard to accept, but it does not make the film anti-Christian but thought provoking.
I am Catholic and was not offended by the film at all, as it raises important issues. What is sad is that it is clear from previous comments on this site is that it went straight over many people's heads.
Read more, attend more University courses, is my advice.