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This is a simple question with a complicated answer, because there are varying degrees of, and reasons for, animosity between any two religious groups. This particular battle is rooted in history. ...
This is a family squabble and it is too bad both sides at times seem obstinate. I was raised as a Catholic, participated wholly in both my faith and religion and am now more of a Protestant. I don't believe the majority of congregations on either side are that far apart, certainly not on the life and death issues and I can attest from personal experience that everything Michael said above is true. Many Catholics I know read & study the Bible now, but generally Catholics view / use the Bible differently than Protestants. I believe canonizing the Apocrypha in the long run has done much harm. It would be a dream come true to have Mass celebrated with the type of preaching available in some of the Protestant churches.
The answer of why there is a dispute or conflict between Catholic and Protestant Churches is very direct and based on a doctrinal position. The Catholic position is based on GRACE being a substance transmittable only via the CHURCH called Catholic, as All Priests have been ordained by someone, ordained by another section of the Church, which traces back to Peter in the beginning. That gives vast authority to a Priest and is not based on the Bible or what God has said or authorized. In the Protestant authority, the fact of Grace is handled by the Holy Spirit when you speak of transmission. It is not by the Pastor or any member, just the Spirit of God. It is based on Faith in God, of which you have NO proven evidence that He exists, other then what you see based on no scientific fact. Example: Life. How can it be that the Atomic structure of all things do not possess life other than names of items set in place in the past? The Atoms of you and the Atoms of water are exactly the same in energy but you have life, logic and knowledge. Only with a super being called God could this have been a factor that caused your Atoms and water Atoms to function differently. Atoms must be created and the fact of Life added to certain one says that God is real. Now you understand Faith. If you had real facts, then Faith would not exist. Jesus is the only one to appear but ONLY in flesh for the purpose of setting in place God's plan of redemption, which is stated in Genesis chapter one and two in the beginning recorded by Jews. There is so much to write about how this is a fact, it would take a book. But you can not explain life without God being true. Hope this helps you to walk by Faith till you return to your creator.
I think that the issue of ordaining a "Vicar of Christ" who's word is law is deeply offensive to many Protestants. Also the mass murders of non-Catholics (Huguenots, Jews etc), selling of indulgences, keeping the Bible away from the people, the incredible corruption of many popes, aid to fleeing Nazi war criminals - the list goes on. Not that Protestants haven't done many wicked things! But the Catholic Church has officially sanctioned much evil. I have no hatred for Catholics and many of my friends are or were Catholic, as was my wife. But the damage done through history is significant. The differences are not just about Mary and hermeneutics.
As someone who has worshipped as a lay minister within various Anglican churches across Great Britain and Ireland (north and south) I think we have much to learn from each other. Catholics and Protestants are brothers and sisters in Christ. As fellow members among God's people (c/f Ephesians 2:19) we should at least dialogue and try to better understand one another. I don't think either group has a complete grasp of the message of scripture and the disciplines involved in its interpretation. As a Protestant I recognise a number of misinterpretations within our churches. More importantly, I think we actually 'need' each other more than we realise.
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