I finished reading the book on the train home tonight. If treated simply as a novel describing the end of the world, the traditional fight of good vs. evil and the only group of Christians in the world who realise what's going in, then it is a reasonable fantasy. Ignoring any religious issues at the moment, there are a few odd ideas in the book such as the passage which described addresses being collected so emails could be sent out to attract visitors to the organisations website. Obviously they meant it in good spirit, but spamming for Jesus would not make them very popular. There was another section towards the end of the book where thousands of voices were singing in different languages but the sounds combined to form the Hallelujah Chorus from The Messiah. If that was tried in a film it would be such a terrible cliche.

Most of the problems stem from the authors notes at the end of each chapter. Oh the whole, these are interesting and draw attention to parallels between the story and the Bible, but again there are a few issues.
In the notes at the end of chapter 4, the 'Big Pot' is used as another name for the Big Dipper constellation, in order to draw another parallel with the Bible. I've never heard this seriously used as a name for the constellation and this sounded so tenuous when I read it.
At the end of chapter 23, the author says:

There is something about the return of Jesus that sounds unbelievable to the modern, cynical mind. And yet it is no more unbelievable than any of the other myths and legends (including evolution) that mankind has come up with to explain our existence.

Now personally, I think the idea that the flora and fauna of our planet has been slowly changing over millions of years to be a more rational explanation than the belief that God created everything in only a few days. For a start it is based on many years of studying the real world, rather than simply believing something which was written in a book a few thousand years ago and for which there is no proof whatsoever.
This absolute belief in every word of the bible is possibly the book's greatest weakness. It crop up again in the notes after chapter 23 where he claims:

Everything else about the Bible indicates that it is an historically accurate book

For most of the Bible, there is no historical corroborating evidence. Especially the story of the creation, where there is absolutely no evidence whatsoever.