The autonomous churches that identify with the Church of Christ are seen as intolerant, sometimes because certain members are really are intolerant bigots, but often just because they have a different paradigm. The idea is pretty basic, that when the church was being built in the New Testament, there was only one church mentioned, and it contained all the saved.
The different paradigm, that causes so much misunderstanding, is that churches of Christ see
themselves as the same as what is mentioned in the New Testament. This does not involve some long,
winding organizational linkage to the original church, but rather the idea that the gospel is a
seed (Lu 8:11), and the church is the same as the original, as long as it is based on the New Testament in the Bible and nothing more. Bible teaching is a high priority, and the result is a lot of members who are able to quote a lot of Bible verses. (This is also the reason for not having instrumental music, or choirs, basketball courts, etc.)
Another result of this different way of looking at things is the perceived intolerance of other Christian groups--member of most Protestant Denominations will generally agree that only those who are members of the church in the Bible, are going to heaven.