The church is located at the bottom of the crater, next to the live atomic bomb around which the town of Megaton was built. The building is two stories high with ramps and walkways all around it and a large, ramshackle sculpture of an atom adorning the roof. These believers pray for a special kind of salvation. You can find out more when you speak to Confessor Cromwell (he's usually standing by the bomb) or Mother Maya (who's usually inside the church). You can generously give a donation (Church Donations) and ask more about this religion and the residents. Cromwell has a key on him, but it's only useful for entering the church at night.
The Church of the Children of the Atom seems to have existed as far back as Megaton's construction, as Manya mentions that they were instrumental in getting the town built. The citizens of Megaton do not mind the cult residing there as their technologies and workforce were needed to build the city, in exchange for it being "built around the bomb."
The Church of the Children of Atom believe the war of 2077 was actually a great holy event perpetuated by their god, Atom.
The Children of Atom believe that each atomic mass contains within it an entire universe, and when an atomic mass is split many universes are created. Therefore, instead of seeing the Great War as destructive, the Church believes it was a creative and unifying holy event. The Children of Atom also see death more as a celebration of life and unification to Atom through "the Glow.", "The Glow" is the earthly embodiment of Atom and the Children of Atom's direct connection to Atom. The Children of Atom view the ghouls as "Atom's forsaken" or those who have unfinished business and, for denying the ghouls their unification with Atom himself, Atom touches them with "the Glow" and asks that they spread the word of Atom to those around the world. Those ghouls that refuse to accept the "gift of the Glow" and refuse to spread the word of Atom are doomed to becoming feral ghouls.
Confessor Cromwell leads the Church and can usually be found preaching outside in front of the bomb. Cromwell will accept donations on behalf of the Church.
Mother Maya is a Child of Atom and wife to Confessor Cromwell.