These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: Underground Zealot
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 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.
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.