Once the church declares you a heretic you will not get a fair hearing. It does not matter how godly you are, how intelligent and how honest, once the hierarchy determines you are a heretic, you will be ignored (See here).
And once the Church adopts a heresy, it is extremely difficult to address it because the heresy is now regarded as “sound doctrine.” (No wonder Satan delights in sowing false doctrines in the church.)
There are 3 main reasons this has happened.
The first is most people in positions of influence in the church have placed understanding above obedience. Understanding is important, we are called to understand; but understanding ought to be the result of obedience, not study (that’s where the Scribes and Pharisees went wrong). The more godly the man, the better the understanding.
“...God works on higher, on divine, on perfect principles, too right for a selfish, unfair, or unloving man to understand.” - George MacDonald
Yes we must read the scriptures; but reading more scripture will only cause you to sink deeper and deeper into error if you are failing to trust and obey God in the simple things (the things that even a small child can understand). If a person fails to put obedience above understanding, their unregenerate mind will cause them to adopt fantastic theories about why God did this, or why he did that, that appeal to the intellect, but undermine faith.
Don’t you know that when you offer yourselves to someone as obedient slaves, you are slaves of the one you obey—whether you are slaves to sin, which leads to death, or to obedience, which leads to righteousness? 17 But thanks be to God that, though you used to be slaves to sin, you have come to obey from your heart the pattern of teaching that has now claimed your allegiance. 18 You have been set free from sin and have become slaves to righteousness (Rom 6:16-18, emphasis added).
Paul is saying that through your obedience you have been set free from sin. There are a lot of verses in the Bible that tell us we will be judged according to what we do; because what we do, reveals our faith, or lack of it.
Anyone who does not provide for their relatives, and especially for their own household, has denied the faith and is worse than an unbeliever (1 Tim 5:8).
Notice that the person who continues to disobey Jesus has denied him, even if they claim to believe in him. The disobedient deny Christ by their actions.
“Distrust is atheism and the barrier to all growth.”
Whenever heresy is mentioned in scripture, disobedience is also mentioned. Heresy is any doctrine that causes people to disobey, turn away from, or ignore Christ. If a person is not encouraging others to disobey Jesus, or are not teaching things that cause others to disobey Jesus, they should not be regarded as a heretic (See here).
If someone is mistaken about a particular doctrine, but they are trusting and obeying Jesus, it will only be a matter of time before they begin to see clearly.
“Obedience is the opener of eyes.” - George MacDonald
Paul had some harsh words for those he regarded as heretics. He warned others not to associate with them. These were people who had abandoned Paul, were not obeying Jesus, and were trying to destroy the church. They were opposing Paul; they were saying he was wrong. This was not a mere theological misunderstanding about a doctrine such as the Trinity (For the Biblical case for the Trinity see Jesus: A Biblical Defence of his Deity by McDowell and Larson; see also Why Believe Jesus Christ is God?).
Because the early Church did not have the New Testament, they regarded the apostles words as having the weight of scripture. So when Paul said something was a sin, for the early Church, that had the same weight as the New Testament has for us today. The early Church was gaining a footing through the teaching of the apostles. No one has the authority to make such pronouncements today. (See here.)
Also, if you read 2 Peter 2 carefully, you will see that what Peter was referring to when he talked about false teachers, is more like what many of us would call cult leaders today. Obedience to Jesus is not an essential part of a false teachers doctrine. (See Am I really a false teacher?)
The second reason is ignoring Jesus teaching on what must be done before a person is excommunicated, as outlined in Matthew 18.
Anything which enforces a binding decision in the church, ought to be governed by the process outlined in Matthew 18:15-20. See The Sinning Brother.
The third reason is a centralised Church.
One might be tempted to think that having a central body which declares what is, and what is not heresy, would make the church more robust, and less vulnerable to heresy. But the opposite is true. It has resulted in the creation of many thousands of denominations. People feel they are simply unable to challenge the central authority, so they think they have no option but to start their own denomination. What is truly sad, is they usually set up their own central authority, which, in time, causes others to break away from them.
Now there is nothing wrong with bishops and elders from different churches getting together and discussing doctrine. They can even put down in writing what they regard as sound doctrine and what they don’t. But this must never be used to ignore what Jesus taught in Matthew 18. The determinations of all church councils are simply the opinions of men, and should be regarded as such. Their decisions are worthy of consideration, but that is all. As often as someone challenges a doctrine with “the Bible says,” the individual, group, or church has to revisit the issue. (It's a little bit like a judge considering the decisions of other judges or the legal opinions of others while hearing a case; a precedent has been set, but that precedent does not have to be followed.) This will result in an extremely well versed and fair minded church which judges all people fairly, and only excommunicates a person after they have followed Jesus commands as outlined in Matthew 18. (In today’s church, the decisions of any church council should never be used to govern the actions of individual churches.)
Now it is true that Paul appointed Timothy and Titus as oversees over multiple churches, but
1. At that time they did not have the New Testament.
2. Because they did not have the New Testament, and they were newly established churches, they were completely dependant on what the apostles told them (see here).
3. If you read the letters to Timothy and Titus carefully you will see they were enforcing the teachings of Paul in his absence. This was only necessary because they were very young churches who were not careful when appointing people to positions of power at the local level. This led to many problems. Paul tells Timothy what kind of people to appoint as bishops and deacons in local churches, but he does not tell Timothy or Titus how to appoint a successor to oversee multiple churches. Their positions existed to give those churches a firm foundation so they could operate independently in the future.
Terrible things happen when churches set up central authorities to govern the affairs of multiple churches.
The Anabapitists were persecuted because of what the “authorities” determined was heresy. Servetus was burnt at the stake because of the authority Calvin had over multiple churches. See A legacy of fear and persecution
Today we have church authorities declaring that it’s ok for clergy to be engaged in certain sexual practices (see here). If you belong to such a denomination you will likely find yourself in a position where you will have to either leave that church, or where that church chooses to leave the denomination.
So how does this look in practice?
If you had to attend a new church, and in a private conversation with a man there, you discovered that he believed something you regard as heresy, would you rather:
(A) Have him talk about your views to the pastor and then have the pastor approach you and tell you that people who hold your views are not welcome in his church
(B) Continue to talk to this individual in private and if unresolved go through the process Jesus outlined in Matthew 18?
A decentralised Church which deals with sinning brothers or sisters the way Jesus commanded has many advantages over a church which is bound to the decisions of a centralised body.
If for some reason such a Church fell into heresy, but still followed what Jesus taught in Matthew 18, they could be corrected by any new comer who was godly and knew the scriptures well. (But they would have to be willing to go through the process Jesus outlined.)
Errors in the church can be corrected when Christians love truth more than their version of Christianity.
“He who begins by loving Christianity more than Truth will proceed by loving his sect or church better than Christianity, and end in loving himself better than all." --Samuel Taylor Coleridge