Frailty (2001) - MAJOR SPOILERS

I watched this for the first time last night. I went into it having no idea what it was about. I mainly watched it for Bill Paxton. Anyway, I have some problems with the ending.

I thought the movie was great when it was about a demented lunatic having his sons help him kill innocent people in the name of God. But by having the twist be that everything the father said was true, I feel that the movie kind of comes off as being pro religious fanaticism. As a rational atheist, I find that to be little irresponsible. I mean what are we supposed to take away from this? That you shouldn't question any hallucinations that you receive from "God"?

Do I have a point here, or am I overthinking what is just supposed to be a creepy fictional story?