An excellent example of flash animation
I have to say your use of layering, direction, and drawing were fabulous. Yet, even a non-religious director tries to get things right. First, Christians do not worship the cross or idolize it as depicted in your film nor do Christians care about the building since the church literally means a group of people not a building.
I loved most of what I saw this is a great piece of work but it does show your ignorance for the religious faith of Christianity. This is one of the least accurate depictions of religion I have seen. He should have been praying upwards or his head bowed to the alter but not bowing and raising as you depicted him which is reminiscent of pagan worship of idols. Yet, your choice of him fighting off evil men is a motif often talked about among protestants and is well done in this piece.
Consider consulting some protestants who can help you make this piece be more accurate. I understand you are not religious but even non-seculars try to follow real examples not ones they think are right.