I've been having a lot of problem with some aspects of the Coptic Orthodox Church. Now I don't know if I can attribute this with the actual Church with a captial C, or just with some prevalent, zealot thoughts which is part of "my stream of Christianity". However, from my limited research on the subject, I found that the Catholic and most of the Orthodox Churches echo the same thoughts.
These thoughts are summarized here: http://www.pravmir.com/what-is-not-church/
In summary this article mentions that we know where the Church is, IE the orthodox church, its sacraments, etc, but I don't know where the Church is not.
Here is a quotation from the article which succicently summarises the prevalent thought:
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“The Wind blows where it will,” Jesus said, “you hear the sound of it, but you do not know where it comes from or where it is going.” I know/know of very Christian men and women who are not Orthodox, yet the “sound” of the Holy Spirit in their lives is so loud that I am almost ashamed to call myself a Christian in comparison. I can criticize aspects of their faith and practice and certainly point out that they are not Orthodox, but to say that they are not somehow part of the Body of Christ, the Church, I cannot say.