In the church that I grew up attending, every Sunday there was an American flag on a staff to the speaker’s right, and a Christian flag on a staff to the speaker’s left.
I didn’t think anything of it. That was just the way it was, and that was the way it was in just about all the other churches that I visited. It wasn’t until later that I came to believe that it was idolatrous.
“Idolatry” is a strong word, and I don’t use it lightly. What convinced me that displaying the American flag in its customary place of prominence in a church was this section of the Flag Code:
When used on a speaker’s platform, the flag, if displayed flat, should be displayed above and behind the speaker. When displayed from a staff in a church or public auditorium, the flag of the United States of America should hold the position of superior prominence, in advance of the audience, and in the position of honor at the clergyman’s or speaker’s right as he faces the audience. Any other flag so displayed should be placed on the left of the clergyman or speaker or to the right of the audience. (italics added)
Displaying the American flag represents allegiance to the United States. Displaying the Christian flag represents allegiance to Jesus Christ. Placing the symbol of allegiance to the United States in a superior place to the symbol of allegiance to Jesus Christ is idolatry, because the Bible tells Christians that Jesus is Lord of all (Ps. 72:8-11; Php. 2:9-11; Rev. 12:5, 19:5). It also says that civil government is a servant of God, and not the other way around (Rom. 13:4; Jer. 25:9). It also says that when God and civil authority are in conflict, that it is God who must be obeyed (Acts 5:29; 1 Ki. 21:2-3).
Many Christians think that there is no conflict between giving honor to the United States and giving honor to God. Personally, I don’t think that there is a problem with giving honor to the United States in the proper context. I have no problem with saying the Pledge of Allegiance, because there is no other country in the world to which I have greater allegiance. I sing the National Anthem at baseball games.
The Flag Code insists that the United States flag must be in the place of highest prominence wherever it is displayed. This means, in my opinion, that it should not be displayed in a place where Jesus Christ is worshiped, because to do so is idolatry.
Elliot Ritzema 
That is very interesting. I never knew that the American law was drafted in that way. I have never really had much problem with flags in church, I have always sort of imagined it as the state coming under the authority of the church. But the American law certainly challenges that perception.