Some think it is not proper that a national flag take precedence over a flag with the Cross of Christ on it inside a church. The US Flag Code cannot not dictate rubrical protocol inside a place of worship. If a denomination or congregation wishes to display both the US and Christian flags and give the right position to the Christian flag that is their business and constitutional right.
Regardless of what people think, there if no "Flag of Christ" only denominational flags. And the Flag Code can and actually does dictate where the American flag should be placed regardless of the venue. And it is a law with penalties. And if you remember correctly, Jesus stated "render to Caesar what is Caesar's". In other words, one should follow the laws of man as well as God's law.