As an atheist, given that people have created religions, prayer seems like a perfectly logical part of them:

"This so called "new religion" is nothing but a pack of weird rituals and chants designed to take away the money of fools. Let us say the Lord's prayer 40 times, but first let's pass the collection plate!"
Reverend Lovejoy

On a serious note, frequent prayer must have a brainwashing effect so if you wanted a religion to last I think it would be necessary.