Keep in mind that in the DCU most metahumans are contemporary to us, not to Jesus.
Keep i mind that in medieval times, demons and witches were believed to be both powerful and metaphysical but they didn't affect faith, just like the mystic priest of other religions didn't convert Jews.
The fact that faith in the DCU is the same as in the real world is canon. Just like the fact that all gods coexist in a mysterious hyerarchy along the New Gods and the Endless. The Presence seems to be Allah/God, maybe portrayed as the actual thing. The Spear of Destiny and the Holy Grail are canon and have mystical properties.
Within that universe, I could definitively see some atheist claiming "about every JLAer died and resurrected, what makes Jesus so special" to which the Christians would reply stuff like "they are all product of science and, some revived through sorcery (as in the sorcery Christians believed witches could do), they were not really dead, etc. and none said they were God, anyway".