Possibly it's the title, because Hacker News has a no-religious-stories clause, but the article itself isn't remotely religious.
I give broad latitude for HN submissions particularly so I can pick up pieces like this. It reminded me of all the times great works of art have made me transcend the human experience. What a feeling! Wow!
I think the flagging system is terribly broken. You got whacked because of the word "God", plain and simple.
I did a 3-part series this summer "Does God Exist?" that examined the proofs for and against the existence of some sort of thing beyond our understanding. I didn't espouse a particular religious view (I really don't have any) and just tried to logically look at the debate from the point of view of being intellectually curious.
Every one of them were flagged. But I submitted all three anyway.
Keep up the good work and don't let the bastards get you down!
It might have been deleted by whoever posted it, auto-deleted if enough people flagged it, or removed by an admin (pg, others?). I have no way of knowing, but it doesn't seem likely that it was flagged off by the community. (Even blatant spam often takes a long time to get flagged; good-faith posts don't generally seem to attract enough flags before they reach the upvote threshold and become immune.)