"Who watches the Watchers" is it anti-christain?

This might be the most pro atheism Episode in trek. I have seen a ongoing theme along these lines in Trek. Since Christianity is the dominate religion in the west it is aimed at christains.
But when it comes to Indians their religon must be treated with respect and dignity.
Voyager treats the injiun Chakotay and his animal spirits like its the real thing.
This vile bigotery on Trek must stop.