When I see someone flying the flag, I absolutely know everything I need to about that person.
That sounds rather prejudice so let me rephrase it in ways that may get my point across.
When I see someone who does not love Jehovah, I absolutely know everything I need to about that person.
When I see someone who calls himself an atheist, I absolutely know everything I need to about that person.
Look, I get it. The confederate flag is associated with a war that has been associated with slavery. Whether rightly or wrongly. But to make a blanket statement like yours ignores everything about the kind of prejudice that everyone on this board has experienced in one form or another.
We run the very risk of becoming no different than the religious institutions and other hate groups that we speak out against simply because they are prejudice to anyone who is different from them. Have you heard of that ridiculous atheism plus movement, they are so much like a religion in their own right that it is nauseating.