Underground Zealot/YMMV

Alternate Character Interpretation: Paul is a jerkass (or does that even count as "alternate"?), Straight has the hots for Paul and is in the closet, Ranold secretly knows Paul is up to something but is just stringing him along, and Barton is an NPO spy.
- Straight is the one who's lying when he says that the Christians killed 'while resisting arrest' were all unarmed. He has more reason to lie about it to Paul than Paul's superiors do.
Designated Hero: Paul, big time.
Designated Villains: The atheists and the government, by and large. While they do seem to want or condone (it's never really made clear which) the large scale murder of followers of any religion, the book points out that every religion except the author's was indeed the cause of World War 3, and since the book demonstrates that the zealots are willing and capable of destroying an entire city if there are enough of them to pray for it, their persecution becomes pretty much justified.
Idiot Plot: Paul is a terrible secret agent, yet nobody is ever suspicious of him.
Rooting for the Empire: While pretty much everyone agrees that the persecution of religious folks in the series is pretty terrible, the Real True Christians™ are quite often sanctimonious asses, and the technological and medical advancements of the "Atheistopia" are undeniably awesome.
Snark Bait
Straw Man Has a Point: After World War III, the UN decided that enough was enough and outlawed the biggest instigator of conflict in the world, religion, and it worked. Meanwhile, the Real True Christians claim that they weren't responsible for World War III and that they're just peaceful people who want a free exchange of ideas, but over and over they demonstrate that they have absolutely no qualms with torturing and killing anyone who believes differently than they do. And they wonder why atheists keep blaming religion for conflict!
Values Dissonance: To pretty much anyone who has anything resembling a shred of human decency. For example:
- The "Christians" are (understandably) upset at their persecution at the hands of the government. So what do they do? Pray for God to dry up the city of Los Angeles, and He does. Jenkins blithely describes how "thousands" of people died as a result. It becomes even more horrifying when you realize that the very old, the very young, and the infirm would be among the first victims.
- Jenkins seems to think that peace on Earth is a bad thing. This mostly has to do with the common dispensationalist conceit that God is irrevocably the only one capable of bringing about peace without having to offset the strife somewhere else. In this case, Atheistopia's peace is displacing conflict into persecution of RTCs. In other words, unless the Tribulation has just passed, "world peace" is self-contradictory.
What an Idiot!: Of special note is the character Andy Pass, who has earned himself the Fan Nickname "the Dork Too Stupid."
The Woobie: Poor Jae. The pain and humiliation she suffers due to her cheating husband Paul pre-conversion is only matched by the emotional abuse he doles out post-conversion.