If Sola Scriptura works why are the Church Fathers Roman Catholics?

I have often pointed out that the primitive church believed and practiced (sometimes more consistently, sometimes less consistently) Sola Scriptura, the principle that, as Irenaeus put it: "We have learned from none others the plan of our salvation, than from those through whom the Gospel has come down to us, which they did at one time proclaim in public, and, at a later period, by the will of God, handed down to us in the Scriptures, to be the ground and pillar of our faith" (Against Heresies, 3.1.1).  Chrysostom explained it this way: "All things are clear and open that are in the divine Scriptures; the necessary things are all plain." (Homily 3 on 2 Thessalonians)  Basil of Caesarea in Letter 283 put it this way: "Enjoying as you do the consolation of the Holy Scriptures, you stand in need neither of my assistance nor of that of anybody else to help you to comprehend your duty. You have the all-sufficient counsel and guidance of the Holy Spirit to lead you to what is right."

The question that we sometimes hear, however, suggests that early Christians or Early Church Fathers were Roman Catholics or Eastern Orthodox.  People will list beliefs that they claim are attested by folks from that early period, including such beliefs as "the sacrifice of the Mass, the Real Presence of Christ in the Eucharist, bishops, priests, baptismal regeneration" and so on.

Before getting to the main response, we must be clear that it simply is not true that the early Christians or Early Church Fathers were Roman Catholics or Eastern Orthodox. This is not the blog post to address all the specific claims, but suffice to say that many of these claims are - at best - misleading.  More crucially, on each of these points, there were a variety of views.  To take an easy example, there are early Christian writers who follow the Scriptural precedent of referring to presbyters and bishops interchangeably.  Those terms (presbyter and bishop), however, came to refer to distinct roles in church government and administration.  Eventually, a more elaborate system with metropolitan bishops and patriarchs develops.  In the West, many centuries later, a papacy develops.  But it was not that way from the beginning.  Moreover, while it is certainly true that the church government of the time of (for example) Athanasius was different from most Protestant churches, it was also different from modern Roman Catholic church government, so it is misleading to say that they were "Roman Catholic" (either in general or on this particular point).    

We could do the same with each of the issues, and we have at various times and in various posts here.

This all misses the main answer to the question, though.  

The main answer is that Sola Scriptura is not intended to, and does not, guarantee doctrinal uniformity.  The fact that there are differences between Presbyterians and Chrysostom should not be surprising, because there are differences between Presbyterians and Baptists.  The differences between Clement of Alexandria and Methodists should not be surprising, because there are differences between Methodists and Lutherans.

Why doesn't Sola Scriptura guarantee doctrinal uniformity?  It is because human beings make mistakes.  Recall the words of the author of Hebrews to his readers:

Hebrews 5:11-14 Of whom we have many things to say, and hard to be uttered, seeing ye are dull of hearing. For when for the time ye ought to be teachers, ye have need that one teach you again which [be] the first principles of the oracles of God; and are become such as have need of milk, and not of strong meat. For every one that useth milk [is] unskilful in the word of righteousness: for he is a babe. But strong meat belongeth to them that are of full age, [even] those who by reason of use have their senses exercised to discern both good and evil.

Likewise, divisions are not because of Scripture, but because of us:

James 4:1 From whence [come] wars and fightings among you? [come they] not hence, [even] of your lusts that war in your members?

And, of course, there is the problem that there is a real temptation to make void the word of God through human tradition.  Jesus rebuked religious leaders in his own day for this.  

Matthew 15:3, 6 But he answered and said unto them, Why do ye also transgress the commandment of God by your tradition? ...  And honour not his father or his mother, [he shall be free]. Thus have ye made the commandment of God of none effect by your tradition.

Mark 7:8-9 For laying aside the commandment of God, ye hold the tradition of men, [as] the washing of pots and cups: and many other such like things ye do. And he said unto them, Full well ye reject the commandment of God, that ye may keep your own tradition.

So, it is not the fault of Scripture nor of the principle of Sola Scriptura that there are doctrinal divisions.  Ultimately, we ought to use Scripture as our standard, because it is the Word of God.

Mat thew 22:29 Jesus answered and said unto them, Ye do err, not knowing the scriptures, nor the power of God.

Scripture is the solution to error, but we should not expect to have a perfect, complete understanding of Scripture (much less of anything not revealed in Scripture) in this lifetime, because there is no such promise from God.