Yes, it is deliberately meant to be Hornblower in Space.

Nick does get a lot more sympathetic as the series progresses - he changes a huge amount over the years. That's part of the strength of the series - we get to see him change. We also get to see his society change (particularly the religious aspects)

We also get to see his society change (particularly the religious aspects)

I wasn't sure whether to be amused or contemptuous when it said that the society was the result of a religious war which allied the Catholics and conservative Protestants against the Charismatics, which seemed ludicrous to me, considering the number of conservative Protestants who consider the Pope to be the antichrist, though I can sort of understand the wanting to wipe out the Charismatics from a political point of view, because they'd be amongst those who would be less likely to submit to a central authority. But then it also had absolutely no mention of any non-Christian religion such as Muslims or Bhuddists. Were they put to the sword as well?

On the other hand, maybe I've been brainwashed by the number of set-in-the-future SF novels which have no mention of religion at all, which is probably equally silly.

I'm hesitant about spoiling - because honestly some of what has disappointed you is more present in later books so eventually you may want to read them - but just for the record - it is actually regarded as a genuine religious miracle which reunited the churches - it's not supposed to have been something that happened at all easily - and the Reunification Church is a very broad one which includes a lot of different denominations among it, with their leaders on a sort of council, and the union is primarily a political one (though many people in Nick's time are very devout, the leadership of the Church generally isn't - they are politicians obsessed with power - in the early books, Nick is blind to the faults of the church leadership, but as time goes on, though he retains his faith, he becomes much more aware of the faults in the organised church of his world, and eventually winds up in conflict with it).

The place of other religions in the world is less clear - Nick really is unusually devout, there are a lot of people who just play lipservice to their faith - but we don't really see much sign of any non-Christian beliefs - except possibly among the Transpop tribes of lower New York.

Considering what was done to the Pentecostals, I wouldn't be at all surprised if other faiths were put to the sword. But we don't really get much detail on that.

I'm hesitant about spoiling - because honestly some of what has disappointed you is more present in later books so eventually you may want to read them

I appreciate the spoilage-avoidance.