Because - sooner or later - their membership dies off and their conviction with them.
(Example? My home church, I'm told, is listed on the bulletin board in the lobby of a small rural congregation in eastern Arkansas under the heading of "scripturally unsound.")
Churches with such a spirit cannot have the Spirit of God.
They display the traits of the man described in Proverbs 18:1:
"He who separates himself seeks his own desire; he quarrels against all sound wisdom."
You can tell them by their fruits: condemnation of others, revoking of fellowship, isolation, a conviction that they are the "only true church." There are other fruits, described in the middle of Galatians 5:20-21:
"... hatred, discord, jealousy, fits of rage, selfish ambition, dissensions, factions and envy ...."
You can see it in their Web sites, when they have them. There will be pages and pages devoted to doctrinal soundness on issues like congregational autonomy, and only a few scattered acknowledgments of the saving grace of Jesus Christ revealed in the gospel story ... if any.
Compare those displays of heart to the ones in the next verse:
"But the fruit of the Spirit is love, joy, peace, patience, kindness, goodness, faithfulness, gentleness and self-control. Against such things there is no law." ~ Galatians 5:22-23
These are not just characteristics of individuals anymore, but have become the culture of entire churches. They survive through the stubborn spectre of fear: each member terrified of a just but merciless God whose wrath might be called down upon them for the slightest infraction (or questioning!) of doctrine by one of their own brothers or sisters!
These churches shrink because most people do not find a life of fear to be attractive, nor something they are willing to sign up for.
Yet they persist because a culture has been established. It has been reinforced through publications and lectures and, now, the Internet.
The overwhelming irony of the "congregational autonomy" they espouse is that it does not restrict them in any way from telling other congregations exactly where they are "wrong" and why they are going to hell!
Some will not cooperate with other congregations - even of their own set of beliefs - because the established culture has declared that to violate congregational autonomy. Better that widows go un-cared for and orphans go hungry and nations go un-taught than to cooperate with other churches in bringing good news to the poor.
This is the sort of behavior that Amos (chapter 5) prophesied about in quoting the Lord as saying:
"I hate, I despise your religious feasts; I cannot stand your assemblies ...." ~ Amos 5:21
The people had denied justice to the righteous and trampled on the poor.
Where do you draw the line on congregational autonomy? Where does your congregation draw it? Because once you invent a term like that, and weave it out of whole cloth, you have to decide how far you will go with it. Will you loom enough to cover yourself completely, a whole suit with hooded veil, so that you are completely cut off from everyone else? Or just enough to cover your butt?
I'm speaking plainly because I believe the time to dance around the subject with polite terms has long since gone.
The Bible talks about kingdom. The apostles talk about kingdom. Jesus talks about kingdom.
That means churches - as outposts of the inbreaking kingdom - need to start seizing territory forcefully, and together, and under the direct operation of the Holy Spirit as revealed in the scripture He inspired.
It cannot be a kingdom if all of the outposts refuse to talk to each other, won't cooperate with each other, won't show respect and love for each other, won't even communicate with each other. Or, worst of all, won't stop biting and devouring each other.
"If a kingdom is divided against itself, that kingdom cannot stand." ~ Mark 3:24
What Jesus said is just as true of God's inbreaking kingdom as it is of the one Satan is trying to establish - and might, if we're just willing to give him a toehold on our hearts.
So I believe it's time for more people to speak boldly and prophetically, like Amos did.
Time to weep like Jeremiah over the lost and the clueless and the rebellious and the isolated-from-God.
Time to speak like Isaiah; with authority about the Messiah who is to come again, and the unity of the Spirit and the bond of peace which must prevail until He does.
Time to proclaim the onrushing day of the Lord, like Joel did.
Time to repent of soft words and soft concepts and soft-heartedness toward the isolationistic and the exclusive and the divisive.
They do not speak softly, and they do not hear soft words over the sound of their own shouting.
Still, there might yet be a few listening who will turn away from the self-centered congregational concept which turns away so many others from Christ.