Two days after 9/11, workers going about the awful task of clearing away rubble and identifying bodies uncovered a 20-foot cross of steel beams, made by the fusing of structural remnants in the heat of the building's collapse. Pictures of it sprang up all over the internet. Workers made a practice of pausing there to pray and leave messages: God has not forgotten us, read one of them. Father Brian Jordan, a Franciscan priest, blessed the cross as a symbol of hope, faith, and healing. Like the Ark of the Covenant, the symbol moved several times over the years but is now slated for a permanent home at the National September 11 Memorial and Museum.

That's where the trouble starts, according to American Atheists, Inc. In a 19-page legal brief filed the last week of...