All nations are under God. But the United States admits it! Some nations do not. Therefore I have no problem seeing an American flag in a church sanctuary.
When I was a Girl Scout, way back in the 50’s, we met in a church. The church had an American flag. We saluted the flag before each meeting. We then opened with prayer. Of course this was in Virginia. Maybe it was different in other states.
When Eisenhower was in the White House “Under God” was added to the pledge of allegiance to prove that we weren’t communist. So I like to see a flag in a sanctuary. To me it means that America is under God.