As a Catholic, I can see how some protestants might see the whole pledging (swearing) allegience to a religious flag thing might conflict with the First Commandment and the whole graven images taboo. I know it's not meant that way, but the concept gives even me the creeps with it's connotations of religious nationalism.
"I am the way, the truth and the life; no one comes to the Father, except through me."
"To as many as received Him, to them He gave the power to become the sons of God, even to as many as believed on His name."