Prayer is more than begging favors from imaginary friends, even if that is the stereotype and there is some truth in it. Like meditation, journaling, and other contemplative practices, it is a mechanism for putting the day-to-day in proper context of some larger narrative. In a theological framework, then, it's about a narrative in which you aren't alone in your joys and sorrows.
I don't think intelligence and spiritual practice are mutually exclusive. I think you can be repulsed by the dogma, indoctrination, and irrationality but also recognize that there might be something redeemable in such popular frameworks for finding meaning and purpose in existence.
The big difference is that meditation and journaling do not require a belief that you are communicating with supernatural beings.
“I don't think intelligence and spiritual practice are mutually exclusive.”
That’s a low bar. At the least we know supernatural/religious beliefs are negatively correlated with scientific training and scientific eminence.
How many people would agree with the statement "prayer works"? How many of them consider that to mean actual concrete effects taking place outside the person making the prayer? It's a lot.
Maybe prayer is, for some people, just a way to organize your thoughts or whatever. But for a huge number of people, it's a way to literally influence outside events.
Maybe put it to the test, even though you feel dumb for doing it, pray for something small that you would not otherwise expect to happen in the immediate future. see what happens
Now, if only we would convince everybody that those supernatural beings don't work through representatives that everybody must listen, that would already be an improvement!
Isn't the inverse also true?
Then there's the type of prayer where you straight up beg for things from FSM for five seconds and move on with your day. Probably less helpful, that.