Idgie was not big on praying. She was in charge of her life, thank you very much, so asking God to intervene in the moments she actually believed in God's existence didn't seem to make much sense. That being said, there were instances that found her praying in spite of herself.
When Bud was standing there, on the tracks, staring wide-eyed at the oncoming train, Idgie prayed. She prayed for a miracle, a time machine, anything at all, but before she could even finish Bud was dead on the tracks, and Idgie gave up prayer.
When Ruth left, Idgie was to angry and hurt to think, much less pray, but some months after, once Ruth was married, Idgie prayed for her, not expecting anything to come of it. She was down by the river at the time, and not far from the tracks. She prayed then because she knew that's what Ruth would have done, and she missed Ruth to the point of implosion. So she prayed for Ruth's happiness.
When Stump earned his nickname, Idgie was praying. First she sees Ruth's son, her son, lying in a puddle of blood next to the tracks and all she can think of is Bud. She's running towards him and muttering a slight plea and when he lifts his head, when she knows he's going to be all right, she prays a quick thank-you, though perhaps that wasn't to God at all.
When Ruth comes back, when she's in the car, Idgie is so happy that maybe she prayed, just maybe. For Ruth.
That night, the night Ruth comes back, when the two of them are together again and alone, Idgie prays again. She prays because Ruth is here, beautiful, wonderful Ruth who she loves more than anyone in the world. She prays because with Ruth's lips on hers, out in the lawn, and later in Ruth's room when there really is nothing between them and she can see all of Ruth and she can feel Ruth against her and she knows Ruth loves her, that night she is certain beyond any doubt that Ruth is a miracle. A living, breathing, heart-racing miracle.