I believe in Church Autonomy, that is, that each individual congregation of believers should be governed by itself. The head of this government should be a group of biblical elders (or overseers) as described by the Apostle Paul in the New Testament (Titus 1:6-9).
The problem with many denominational congregations is that they are not autonomous. They are often united and governed by an organization or convention of leaders that rule from afar, detached from the local congregation. While it is true that these organizations for the most part allow individual congregations to regulate themselves, they reserve the power to step in whenever they wish to alter or change any congregation that considers itself under their authority.
This is not a good thing. Each congregation of believers ought to govern itself by the leadership of its own elders. Only those that live in the area and personally know the needs, strengths and weaknesses of the people are qualified to lead any given congregation.
Many believe that belonging to an organization is necessary to accomplish the goal of spreading the gospel, because no single congregation has the means to carry out the task alone. While I agree no single congregation has the means alone, I do not agree that forming some kind of confederation is the only solution. Many autonomous congregations are able, despite their independence, to combine their resources and work together to send missionaries and aid to those in need without forming a binding confederation.
The congregations collectively known as the Church of Christ, for example, are totally autonomous. There is no earthly authority greater than an individual congregation’s elders. The decisions of one of these congregations do not affect the other congregations. If the people of a congregation believe the elders are not leading the church correctly according to Scripture and no agreement can be made, then those people can leave that congregation to form a new one that is completely independent. Among the Churches of Christ, this is not seen as a bad thing but necessary to the growth of the Church. Many in the Church of Christ are well aware that power corrupts, and a group of elders becoming corrupt is bound to happen from time to time. When it does, the people need to be able to separate and form a new congregation. There is nothing unbiblical about this.
On the other side, a congregation of believers whose overseers are hundreds of miles away can barely even make a complaint known to them, much less have it addressed. In the end the believers are beholden to the whims of the organization, and if that organization becomes corrupt, which is inevitable in human society, the believers are hopelessly bound to the organization unless they decide to become independent. The problem with this is that these believers have also become dependant on the organization, and feel they cannot survive on their own, much like an abused spouse feels she cannot leave the marriage due to her co-dependence on her husband.
Most Protestants understand how the Roman Catholic Church fell into the state it is in today, but fail to realize that their own congregations are headed down the same path. By allowing a few detached people to rule over many churches, you give them power with little responsibility or accountability. Over time, their lust for power will corrupt the system, and eventually each and every one of these organizations, or denominations, will become more or less exactly like the Roman Catholic Church. If you do not believe me, simply study the history of the Roman Catholic Church.
In the first few centuries, churches were autonomous. Then Constantine demanded the churches be united together under a single group of bishops. Then that group of bishops esteemed one of them above the others, an office which has become known as the Pope. Over time, the power delegated to the Pope was so immense, the office became hopelessly corrupted. Now the Pope is considered infallible, capable of both granting salvation and rescinding it, things only God Himself can do. The Pope has re-written the Bible time and time again to suit his own desires with his papal decrees and documents.
No believer is more important or better than another. All are equal in Christ. It is true that God appoints some to be leaders, some to be servants, but we are all equal in the eyes of God. Each of us can read and study our Bible, and if we see our leaders are not leading according to Scripture, it is our duty as Christians to address this and seek to either turn our elders back to the truth, have them resign their posts, or, if necessary, to start a new congregation with new elders based on the Scriptural authority of the Word.