Some personal exposure is required here (no not that).
I don't question things to be awkward or rain on any parades. I do so because I have to. As a child my mother tried to instill "table manners" in me. She failed, mostly. I couldn't see the point of using one particular utensil over another if either did the job, and demanded an explanation of why it mattered. Of course she couldn't come up with anything, because, at bottom there is no such reason. "Because people do" is semantically null to me.
This just one example. I have an insatiable curiosity, and a disinclination to accept anything that doesn't make sense to me. So it's always, why, how? So if you say that accepting a falsehood (like the prayer causing the rain) is acceptable it's just gibberish to me. Why would anyone believe anything that was not strictly true? "If ignorance is bliss, 'tis folly to be wise" ... that has some attraction, and even makes sense to some extent, but I can't do it. Can't not won't. Would I be happier "ignorant"? Probably, but I CAN'T.
I do try not to be rude, or hurt people's feelings and have, with advancing years, walked away from many confrontations that I would never have done at one time.
The following true story may help. I once "tested" religious belief by asking "god" to tell me if he existed. It seemed to my logical mind that if a "person" exists then the best way to get answers about that person is to ask them, not rely on the beliefs of others or ancient documents. To my surprise, I got an answer, though not in words. Here's the point. All I "believed" at that stage was that "something" had communicated with me. All the rest was to be determined. I then proceeded stepwise, asking for knowledge to be revealed bit by bit. I spent some time as a member of a Christian church, but never came to believe the basic stuff like salvation, trinity, virgin birth and so on. Eventually it faded away. I can only conclude that I somehow cooked it all up in my mind.