I posted recently about the custom of removing shoes in some Christian churches. A week ago, I came across a forum discussion about the Coptic practice:
Orthodox Christianity.net: Scarves Worn During Communion and no shoes a Must for Women??
The Coptic tradition is to remove shoes before entering the sanctuary of the church to receive communion. The original post complains that this results in walking on a floor that is wet and dirty. This seems an understandable complaint; it is not always nice to walk shoeless on a floor that has been walked on by dirty shoes.
The obvious solution would be for the congregation to remove shoes before entering the church, so that the whole carpeted area stays clean. Perhaps they don't do that because they want to emphasize that the sanctuary is the most holy area of the church.