The basic premise of the article, repeated multiple times, is that the root causes is the rejection of the authority of the traditional Church, and adherance to it’s teachings.
Spirited: The essay speaks of many things: the true meaning of liberty, the nature of man, the existence of the transcendent, the existence of a spirit theater, the existence of man’s soul and the truth that he is made in the spiritual image of his Creator, the real existence of both heaven and hell, the mystery of man’s will, the pathological lies of Marx, et al, and much more besides.
Yet you’ve reduced the many issues the essayist speaks of to one absolutely false conclusion. Yes, the writer mentions the Church in passing as one of the reasons behind the rebellion. It is you who have falsely elevated the ‘mere mention’ to the absolute ‘be-all-end-all.
The article is rife with scriptural references presented as evidence to back up her arguments. The religiosity of the article involves a lot more than "mentioning the Church in passing".
Tl's entire point here is to make Paine's rejection a religious issue, that is that he was rejected for being an atheist, not for any other reason.
The simmering resentment against religion and Christianity in particular, is what leads to these kinds of accusations that this is all about a religious litmus test.
It certainly appears that tl would LIKE it to be about rejecting the authority of the traditional Church, although which church that is would be nice to know, because then it would be so easy to hurl slurs and rail against theocracies, bigotry, and intolerance that religion causes, thus providing justification for attacking it.
By couching it in terms of religious persecution, Paine, and other atheists, can then become the modern day martyrs, persecuted for their ideologies, beliefs as it were, by the evil religionists (read Christians).