Cardinal Newman recognized the obvious difference between the current Roman Church and the early church. He was too deep in history not to see it. He had to develop his famous idea of doctrinal development to explain it. He argued that all the later Roman doctrines and practices were “hidden” in the church from the beginning. They were made explicit over time under the guidance of the Spirit. But the problem that many Roman Catholics fail to see is that there is a difference between development and contradiction. It is one thing to use different language to teach something the church has always taught (e.g., the “Trinity”). It is another thing altogether to begin teaching something that the church always denied (e.g., papal supremacy or infallibility). Those doctrines in particular were built on multitudes of forgeries.Dr. Mathison is just flatly wrong here. Let us take a look at these two examples which he specifically mentions. Keep in mind, he is stating that not only are these "built on multitudes of forgeries," but that they are also not "developed" doctrines - rather they are "contradictory" doctrines (to the false concept of sola scriptura, which is the invented doctrine of the Protestants of the 16th century).
The basis of papal supremacy is built upon the Scriptures themselves! One who adheres to Scripture should not oppose that for which Scripture is the foundation! Now Dr. Mathison does not get into examples in his article, rather he just makes an unsubstantiated assertion. I will not respond in kind, I will present evidence from Scripture for the foundation of papal supremacy.
Matthew 16:18-19 - I'm sure most reading this already have heard the arguments from both side as to whether or not the Church would be built upon St. Peter or upon his confession, so I won't belabor that particular argumentation here and now - the fact of the matter is that Jesus is speaking directly and solely to St. Peter here, and against that - there is no argument. St. Peter is singled out here and to him alone the promise of the keys to the kingdom of Heaven is given.
Isaiah 22:20-21 - There is a Biblical analogy for just as King Hezekiah (715-686 B.C.) gave authority to his Prime Minister Eliakim (Isa 22: 20-21), so too did Jesus invest Peter.
Rev 3: 7, refers to “The words of the holy one, who has the keys of David, who opens and no one shall shut, who shuts and no one opens.” These are the royal keys Christ presented to Peter.
John 21:15-19 - Jesus, in threefold manner, while still maintaining the "sheep" are "His," gives to St. Peter, and St. Peter alone, the commission to "feed My sheep...tend My sheep..." Whereas Jesus remains the Shepherd, He is passing on His authority as such to St. Peter.
Now, there are many more references which can be shown here - and while I do not deny Protestants have their own "spin" on them, the fact remains the concept of papal supremacy is rooted in Scripture. Just because someone, like Mathison, can come up with alternate interpretations of Scripture passages - this does not negate and certainly does not make the Catholic interpretation contrary to the Scriptures appealed to. He may be able to disagree with our interpretation, but he cannot deny the scriptural foundation of this teaching.
This is also based in Scripture and thus cannot possibly be considered contradictory, nor based in forgeries which came about hundreds of years later. This again brings us back to Matthew 16:18-19. Now Jesus did not limit what St. Peter, alone in this context, could bind or loose - in fact He says to him, "whatsoever you shall bind..." which is not mere implication, but an explicit statement of affirmation that whatsoever St. Peter chose to bind or loose on Earth was also bound or loosed in Heaven! I will presume that Dr. Mathison would agree with me that nothing fallible could possibly be bound or loosed in Heaven, therefore this authority given to St. Peter, alone, in this context is infallible authority! It is not based in any forgeries which came about centuries later - but in Jesus' own words!
Were there forgeries? Yes, we cannot deny that these existed and I have given a much fuller response to these in a previous article. Again I must assert that these forgeries were not the foundation of either papal supremacy or infallibility. Those who look objectively to both history and the Scriptures, I am quite confident, must come to the same conclusions as I have and utterly reject Dr. Mathison's premises that papal supremacy and infallibility are not only not contradictory - but also not built upon the forgeries which came centuries later.
 Qtd. from http://www.catholicfaithandreason.org/papal-supremacy-in-the-bible-and-church-fathers.html
 The Papacy and the False Decretals (a response to William Webster): http://www.americancatholictruthsociety.com/webster/decretal.htm