Makes sense to me. See what you think.
[A]ccording to American flag etiquette (yes, there are people who specialize in that), it is okay to fly the U.S. flag upside down (as a signal of distress), at half mast (mourning) and alongside other national flags in certain spaces such as at the United Nations headquarters in New York. But it is never okay to fly it “in submission” to something else—for example lower than another flag in the same space. According to my friend who is also a scholar of Christian worship and has taught graduate level course in Christian worship for many years, having the U.S. flag in any worship space is wrong because it is “being flown in submission”—to God.
A very interesting conundrum to consider.
The point is that the worship space, the sanctuary (whatever it is called), is dedicated to sole worship of God above all else. The people gathered are ostensibly worshiping God alone and expressing their supreme loyalty to God, Jesus Christ, the Kingdom of God. Having the national flag in the same space violates flag etiquette because it is flying it “in submission.” It should only be flown where nothing else is being placed above it in terms of importance.