In its accompanying commentary on the document, the CDF observes:
The fifth question asks why the ecclesial Communities originating from the Reformation are not recognised as ‘Churches’.
In response to this question the document recognises that “the wound is still more profound in those ecclesial communities which have not preserved the apostolic succession or the valid celebration of the eucharist”. For this reason they are “not Churches in the proper sense of the word” but rather, as is attested in conciliar and postconciliar teaching, they are “ecclesial Communities”.
Despite the fact that this teaching has created no little distress in the communities concerned and even amongst some Catholics, it is nevertheless difficult to see how the title of “Church” could possibly be attributed to them, given that they do not accept the theological notion of the Church in the Catholic sense and that they lack elements considered essential to the Catholic Church.
In saying this, however, it must be remembered that these said ecclesial Communities, by virtue of the diverse elements of sanctification and truth really present in them, undoubtedly possess as such an ecclesial character and consequently a salvific significance.
To me, the interesting question here is why "they do not accept the theological notion of the Church in the Catholic sense." Experience has led me to find the following commentary from a prominent ex-Catholic, Roland Martin of CNN, most revealing. It is not the most theologically sophisticated, but it is common enough to exhibit the operative ecclesiology of most Protestants.
You can read the whole thing for yourself, but here's the heart of it (emphasis added):...what ticked folks off was his assertion in the 16-page document by the Vatican's Congregation for the Doctrine of the Faith that the only denominations that can call themselves true churches are ones that can trace their roots back to Jesus Christ's original apostles. He even suggested they suffer from defects.
This is nothing but a naked attempt by Pope Benedict XVI to "own" Jesus by virtue of the Catholic Church considering the apostle Peter as its leader. He refuses to acknowledge the reality that Jesus didn't consider a church to be most important. What was? The Great Commission.
The Bible records in Matthew 28:16 that Jesus called his 11 disciples (the other, Judas, hanged himself after betraying Jesus) to Mount Galilee and decreed, "All authority in heaven and on earth has been given to me. Therefore go and make disciples of all nations, baptizing them in the name of the Father and of the Son and of the Holy Spirit, and teaching them to obey everything I have commanded you. And surely I am with you always, to the very end of the age." (New International Version).
It doesn't matter what Pope Benedict XVI has to say, or for that matter, any other religious leader. A Christian believes in Jesus Christ and what He had to say, not what a man of God has to say. This is not an attempt to completely dismiss religious leaders, but is further evidence of what happens when ego is more important than the work of Christ.
John 14:6 says, "I am the way and the truth and the life. No one comes to the Father except through me." Nowhere does it say that Peter, Pope Benedict XVI or anyone else can supplant Jesus as the leader of the church.
It is these kinds of missives by Pope Benedict XVI that do nothing to support or build the community of faith. All it does is divide.
Leaving aside the insulting suggestion that the Pope, one of the most distinguished theologians of the age, is just an egotist, the interesting thing here is Martin's vision of what it is to be church. It is typically Protestant. In that vision, the Church is not the Mystical Body of Christ in which, among other things, his headship over her is embodied by an ordained hierarchy to whom he has granted real authority direct from himself. No, a church is only a voluntary association of people who follow and proclaim, or believe themselves to follow and proclaim, Christ himself. Now a church, whatever else it may be, is at least that. On that much, the Pope can agree with the Roland Martins of the world. But if church is understood to be only that, then it is at bottom a human creation. The constitution or polity of such a church is a creation of its members, and the leaders within such a setup hold and exercise only so much authority as the membership chooses, explicitly or tacitly, to permit them. If what such "men of God" have to say does not, in the view of some or most members, match what Jesus Christ has to say, then those members should ignore or replace such leaders—or, if necessary, bypass them by founding a new "church" with leaders more faithful to what is deemed to be the truth. Any leader who pretends to a greater authority than that is the victim of their own ego, and as such accomplishes only division among the brethren.Ironically, however, it is a corollary of such a vision that every man, in Luther's words, has "a pope in his belly." If there is no God-given authority within the church to tell us infallibly and irreformably what Scripture means and what the deposit of faith accordingly is, then we are each left to something less than the Church to determine what Scripture means and what the deposit of faith accordingly is. A given "church" may say it acknowledges the authority and infallibility of divinely inspired Scripture; many do just that; but the endless fragmentation of Protestantism amply demonstrates one of the Pontificator's Laws: "When Scripture alone is one's authority, Scripture ceases to be one's authority." Thus and ultimately, the only authority for resolving disputes about faith and morals is what Newman termed "private judgment," which can be purely individual but which, more typically, is that of a party or local church over against the church catholic. I do not, because I cannot, believe that that is what characterizes the church founded by Jesus Christ. For private judgment yields only human opinion, not the virtue of faith; hence it precludes the assent of faith as distinct from opinion, thus precluding the only appropriate response to divine revelation and the necessary attitude of the member of the Church as such. A church based on private judgment, and thus on mere human opinion, is not only a sign but a guarantor of disunity—the opposite of that unity which it is the special charism of the Petrine ministry to ensure. It is not the Church founded by the Lord himself.
True ecumenism requires Peter. Otherwise it's just a negotiation.