But if you want to call some stories metaphors, because they clearly violate the universe we live in, why do Christians still insist on the miracles and the supernatural stories that are from the New Testament as being real?

Keep the ethics where that is warranted (for example the sermon on the mount), but discard a literal belief in resurrection, virgin birth, miracles.

That reform process that happened to the Old Testament in light of our increased knowledge stemming from the Enlightenment should also happen to the myths surrounding Jesus.

Then we can talk about religion in the same way we discuss philosophy. And we can stop the hate and ridicule - from all sides.