It can only imply endorsement of national policies if the church endorses those policies, or remains silent about those it opposes.
The swastika flag in German churches at that time should have been a constant reminder of what the church stood in opposition to, even if they could not oppose it overtly.
I likely disagree with this Methodist leader on much of what the church should oppose in our government. I also disagree that removing the flag is the right approach.
If you don't agree with what your government is doing, it's your responsibility to do what you can to change it. Christianity teaches us to be moral members of society. While Christianity does teach forgiveness of the repentant, it also teaches personal accountability.
Much of the Church seems to have forgotten that forgiveness is something that comes in response to repentance and has abandoned the concept of personal responsibility for sinful actions.
IF my church removes the US flag from the dais, I’m leaving the church, AFTER I have my say on the issue.