Early Church Organization
Many people think that the Catholic Church was the earliest Church but according to historical record that would be either the Coptic or Syriac Church. There were originally supposed to be different churches, according to the major cities arranged geographically. Rome was the least important at first and only chosen because it was the western imperial capitol. The other major centers were in Antioch because it was an important commercial center, Alexandria because it was an important educational center and Constantinople because it was the more important eastern capitol of the Roman Empire (with Jerusalem being a merely symbolic one).
The Church of the East was centered near modern day Baghdad as it was the capitol of the Persian Empire. Because of rivalry between the Persian and Roman Empires, tolerance for Christianity in Iran would only exist if they made a clean break with the Church in the Roman Empire. They had to make up a heresy to do so and that is why they are not represented in some of the early church councils. Recently the Catholic Pope apologized to these Oriental Orthodox churches and admitted that they were doctrinally correct and the differences came from different explanations for the same doctrine (the Trinity) in different languages.
The Middle East was the center of most of Christianity, until the time of the Crusades. This was the halfway point in the history of Christianity. Doctrine was supposed to be determined by counsels, with a representatives from each of the regional churches. The Protestants did not exist, until about the time of the Renaissance - the 3/4 point of Church history. Similar to today, politics and religion were inseparable in a practical and public sense. A lot of things were changing at the time and the Church was too powerful and became corrupt about the time of the Crusades.
Overview of Reformation
The Protestant Reformation was only part of a much longer struggle to reform the Church that started at the time of the Franciscan order (started by Saint Francis). There were struggles within the Protestant church up until about the 1990s to continue to further define what the church should be and what relationship the leaders and members were to have with each other and God. Along the way, there were major battles with Islam, Catholicism, and other Protestants that were sometimes full wars and sometimes mostly institutional, spiritual, or political conflicts.
There is a recurring theme within the Protestant Churches about trying to be just like the Church at the time of the New Testament. It is hard to get much information on this time period in Church history outside of the Bible because of the intense persecution. What we do know from the Letters to the Churches from Paul and the other Apostles is that most of the same problems we have today in the Church were also problems at that time as well.
The issues the Protestants brought up look like issues relevant for their time and place in geography and history. It made the Church powerful enough to survive against the major Islamic empires of the Early Modern World and later Modern Atheism which came out of the European Enlightenment. It is very important to stick to the fundamentals and at the same time adopt as many cultural elements that are consistent with the Gospel message.
The Reformation was successful, unlike other similar reform movements because there was a long standing feud between the Holy Roman Empire and the Pope. The pope was called the anti Christ as early as 1200 AD centuries before being described that way by Reformation leaders. France at the time was fighting for its very existence and the real power in Europe was with the Habsburgs not the Pope.
Reformation Politics
The Habsburgs controlled at one time all of both the Spanish and Portuguese Empires at their height, as well as what is now Germany, Austria, Hungary, and Belgium. The French made three major decisions to deal with this. They funded the Protestant movement in the Holy Roman Empire, they made an alliance with the Ottoman Empire, and they made most of the Protestants in France leave, many of which ended up in British and Dutch colonies.
One of the reasons why the English and Dutch both did so well is that they united for over a hundred years. The Dutch managed to pull the Portuguese into the biggest religious war ever so that they took some of the best parts of the Portuguese colonies including South Africa and the Indonesia (the spice islands). The Dutch and English avoided many wars in Europe and controlled their finances better. If these things and many more very lucky things hadn’t happened at just the right times there is no way the British would ever have become a world power.
Money and wars are very related as most the money in governments has traditionally been spent on wars. At the same time that France allied with the Ottoman Empire, the Ottoman Empire was invading Europe from the other side. A coalition of mostly Catholic armies from the Habsburgs Empire and the Polish-Lithuanian Commonwealth held them back over hundreds of years. Ivan the Terrible and Vlad the Impaler were very helpful as well. At two different times, the Ottoman Empire laid siege to Vienna, which was the eastern capitol of the Habsburg Empire. The next logical country to invade would be France.
There were many major wars between the Protestants and Catholics until the 19th century when Napoleon destroyed the Catholic Church by looting all its money from Europe to finance his campaign to destroy Spain and Portugal and create modern Germany and Italy. At the end of the Napoleon Wars, the Austrian Habsburgs convinced the British that a cease fire between European countries would be best for everyone in Europe. The peace broke as World War 1 started.
Since then some missionaries mostly from the United States and the United Kingdom spread the Gospel to several former slaves and then they brought the Gospel to millions in Africa. Today, the center of the future church is in Africa and Asia. There are now missionaries going back to Europe to reintroduce the Gospel to the some of the same countries that brought the Gospel to them. Ironically, the little left of the Church in Europe is mostly Catholic. Also the biggest Churches in Africa are not Evangelical or Pentecostal but independent of major Western denominations as well as a large number being Catholic or Anglican.
Reformation Doctrine
Doctrinally the major differences between most Protestant and most Catholics historically has been related to the fact that the Catholic Church had inherited a lot of cultural things from the Roman Empire that were no longer relevant to Northern Europe. The Roman Empire was notorious for never compromising, it was very elitist, and was very patriotic. Translating the Bible to the emerging languages of the what would be the dominant World Powers for the next several hundreds years helped make these countries independent of each other.
Getting rid of the previous bureaucracy allowed them to further distance themselves from other rival powers and win friends with the local population and inspire patriotism to get more conscripts to fight in their wars. By making the faith an inward and personal one they were no longer bound by what someone in Rome told them to do. They could continue to then make changes indefinitely, without having to be bound by previous decisions by starting new churches.
So what is a good Christian to do about this? Learn your culture well and understand the Bible well. Combine them in appropriate ways. Traditions are good but they should not become more important than the Bible.
You can only go so far with doctrines developed by different churches. Pray frequently, get involved in the Church, study the Bible, spread the Gospel, help people in need and define your faith through action. Let God be your Lord and let Him make you into a better person.