Some background to maybe keep you reading, before I get into why I think there should be no flags. My dad served for almost 30 years in the US Air 
Force. I server for 13 years in the USAF Reserves. I have lost friends and do whatever I can to support our military. I was even the president of the Randolph AFB Air Power Community Council. I served proudly and continue to show support whenever I can. I am also the one that stops and stands during the national anthem every time I hear it. If I can’t stand, I will stop talking. I am a proud vet and American.
That said, I do not believe that flags belong in the Sanctuary of a church.
First, let me define sanctuary in the Catholic sense. In the front of the Church at the first step up you begin to enter the Sanctuary. If there are no steps, it should not be visible when focused on Altar or Ambo. I don’t mind a flag in the body or back of church, but not in the sacred space where the sacrifice for the mass occurs.
Why?
First and foremost, what we are doing at our liturgies is so important that it needs to be our only focus. The flag remains a powerful symbol and conjures up many things not related to the transformative act of Eucharist that we celebrate together. Our focus my be laser tight on what we are doing at the altar.
Second is that our worship is open to all people of all countries and say for a former USSR member seeing the US flag could have very mixed feelings. All are welcome to the celebration and nothing should inhibit their full participation in the celebration. What about a family that just lost a loved one in a war, and the last flag they saw was draped on their loved ones casket. Is that what they need to be reminded of at Mass right next to the Altar?
So not no flags anywhere, just away from altar and Ambo.
I am not alone in this, but it is such a hot topic the US Bishops have been wishy washy at best. I wrote this in a bulletin once and you would have thought that I was asking for everyone’s first born.
Just my opinion, no flags in the sanctuary. On the 4th of July, line the parking lot, have them at doors and even sing a patriotic hymn, but please don’t have them in a place sharing the focus of the Mass.
This was outstanding.
I am okay with no flags at all in the church.
Im the Gospel of Mark, Jesus’ focus was building the Kingdom of God on Earth. His idea was not to elbow His way into the existing government structures, but to change people’s focus entirely. To give onto Caesar what is Caesar’s and give onto God what is God’s. You could say that he was the original proponent of the separation of church and state.
Second, I think that Christians should self-identify as Christians first, not their nationality. I remember seeing a parody news show where the reporter was talking about an airline crash where there were no survivors and then said, “Fortunay, there were no Americans aboard.” Isn’t that the way most of us see the world? Christ calls us to care just as much about a terrorism death in Baghdad as we do for one in France, a flooding victim in Bangladesh as in Louisiana, etc. My observation is that flags create virtual walls (and maybe soon real walls too) that make us indifferent to the suffering of others. My hope would be that an absence of flags in a church would help communicate that Jesus calls us to love ALL people equally regardless of nationality, religion, race, etc.
Finally, no country in history has had a spotless record. And while the United States has a comparatively excellent record, we still have things in our history that will always be moral scars. Slavery, Jim Crow, red lining, the internment and confiscation of land of US citizens of Japanese decent, etc., etc. are also part of what is otherwise a pretty stellar history. This said, we need to have the moral courage to speak out when we lose our way. And having a flag-neutral space allows us to better form our moral conscience first as Christians, apart from the political winds of this country.
Man, my parents are both gone and two of the best “responders” to my posts are my brother and sister, and guess what, that is it, not more siblings!