Argument from Universality: When the Ad Populum and Chronological Fallacies Aren't Fallacies

ruthful lips endure forever, but a lying tongue lasts only a moment.  Proverbs 12:19

The Catholic Church's Universality is a good reason (all other things being equal) for people who are already Christians to believe she is the True Church that Christ spoke about when he said

"Upon this rock I will build My Church; and the gates of Hades will not overpower it." Mat. 16:18

and

"I have much more to say to you, more than you can now bear.  But when he, the spirit of truth, comes, he will guide you into all truth."  John 16:12-13

Living in America, a strange place where Protestants happen to be the largest religious group (but maybe not for long), it is easy to lose sight of the larger scope of History and the promises of Christ that the Church would never fail, and that the Holy Spirit would always be with the Church.  

It would be fallacious to argue simply from an institution's age and numbers that its teaching is correct.  These are known as the chronological and ad populum fallacies, respectively.  But the very nature of the Church is to be universal, worldwide, and given that the Catholic Church best fits this description, it makes it more probable, based on scripture, that the Catholic Church fulfills this role:  

“My prayer is not for them alone. I pray also for those who will believe in me through their message, that all of them may be one, Father, just as you are in me and I am in you. May they also be in us so that the world may believe that you have sent me. I have given them the glory that you gave me, that they may be one as we are one: I in them and you in me. May they be brought to complete unity to let the world know that you sent me and have loved them even as you have loved me. Jn. 17:20-3

Is it not logical to conclude from what Christ says above, that since the beginning of the Christian Era, when Jesus sent the Holy Spirit to the Apostles at Pentecost, somewhere on Earth, at every point in time, there have been Christians who were taught what Christ wanted them to believe?  Yet, for at least 500 years, historians agree the only nominal Christians around were Catholic Christians, Assyrians and Oriental Orthodox Christians, all of whom have a lot in common, but very little in common with modern Protestantism.  Consider this historical graph of denominations that endure to this day.

Again, one of the best arguments atheists have against Christians is that if there are so many Christianities that significantly contradict one another, yet they affirm a book that says "they should all be one," then they are all wrong and hypocrits.

Yet, when one considers the myriad of divided tiny sects in the World, a theme emerges.  Consider the summary page wikipedia provides here. Now (please somebody correct me if I'm miscalculating or miscategorizing here), if we group together Churches in doctrinal unity with commonly acknowledged leaders and authority structure, we get the following:

The only way Christians within these communities differ is in their customs, but they all share a leadership body and confess the same doctrine about Baptism, Eucharist, Bishops/Pastors, Justification, etc.  On the other hand, the Protestant Churches mentioned under, say, Presbyterianism, differ radically on important points of doctrine like gay marriage, male-only priesthood, etc.

It is true that there are about 700 million Protestants, but they have no common beliefs aside from protesting against the Catholic Church from which they sprung and acknowledging Christ as messiah (although Unitarians for example might even differ on this claim if it entails giving Christ any unique status).  If you're a typical Protestant, the truth is that the vast majority of Christians who are, and the vast majority of Christians who ever were, are in agreement with each other, but differ very significantly from you on important points of Christian belief like the Eucharist, the Liturgy of the Church, and the role of Bishops as the leaders of the Church who must be ordained by a previous bishop in succession back to the apostles and Christ.

It is true that the Protestant might be correct, if we only consider the arguments on this basis, but the burden of truth surely falls upon you, O Protestant, in light of this evidence.  Furthermore, when Christ says the gates of hell shall not prevail against his Church, he seems to be implying that the true believers will endure from his time on Earth to the end of time.  While we may not have perfect records of the primitive Church's practices, we do know that for Centuries, all Christians acknowledged the succession of Bishops and the presence of Christ in the Eucharist.  It is not the Catholic Church that is weird, aberrant or heretical by historical standards.  Protestants are the aberration from historical Catholic unity.  You may hope that these historical trends will change and that your small sect will sweep the world the way only Catholic Christianity and Islam (which if we divide into Shiites and Sunnis are still much smaller than the Catholic Church) have been able to do to date.  Atheists who claim that the Christian witness is too divided to take seriously similarly suffer from provincial (usually American or British) ignorance about the composition of the Christian world and historical ignorance about the development of Christianity.

Catholic Christians can be confident that overwhelmingly, the Catholic Church has always been the voice of Jesus on Earth on all points of doctrine, leading God's people to the true interpretation of Scripture and Tradition by the inspiration of the Spirit of Truth that Christ promised.