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From Haydock’s Scriptural Commentary:
Ver. 16. All scripture divinely inspired is profitable to teach, to reprove, to correct, or admonish, to instruct others in justice, and in the ways of virtue, that thus he who is a man of God, a minister of the gospel, may be perfect and instructed unto every good work. But when our adversaries of the pretended reformation, undertake from these four verses to shew, first, that every ignorant man or woman is hereby warranted to read and put what construction his or her private spirit, or private judgment, suggests upon all places of the holy Scriptures; and secondly, that the Scriptures alone contain all truths which a Christian is bound to believe; or at least, that the Scriptures teach him all things necessary to salvation, without regard to the interpretation and authority of the Catholic Church: I may at least say (without examining at present any other pretended grounds of these assertions) that these consequences are very remote from the text and sense of St. Paul in this place. As to the first, does this follow; the Scriptures must be read by Timothy, a priest, a bishop, a man of God, a minister of the gospel, whose office it is to instruct and convert others, therefore they are proper to be read and expounded by every ignorant man or woman? Does not St. Paul say elsewhere, (2 Corinthians ii. 17.) that many adulterate and corrupt the word of God? does not St. Peter tell us also, (2 Peter iii. 16.) that in St. Paul’s epistles are some things....which the unlearned and unstable wrest, as also the other scriptures, to their own perdition? See the preface to the Gospel of St. John, where reasons are brought for which it was requisite that the Church should put some restraint to the abuse which the ignorant made of reading the Scriptures in vulgar tongues. As to the second consequence, does it follow: every Scripture divinely inspired is profitable for St. Timothy, for a priest, a bishop, a man of God, a minister and preacher of the gospel, to teach and instruct, and conduce to bring both him and others to salvation; therefore they contain all things that a Christian need to believe? &c. Is not every Christian bound to believe that the books in the canon of the New and Old Testament are of divine authority, as in particular these two epistles of St. Paul to Timothy? Where does the Scripture assure us of this? But of this elsewhere. (Witham) -— Every part of divine Scripture is certainly profitable for all these ends. But if we would have the whole rule of Christian faith and practice, we must not be content with those Scriptures which Timothy knew from his infancy, (that is, with the Old Testament alone) nor yet with the New Testament, without taking along with it the traditions of the apostles and the interpretation of the Church, to which the apostles delivered both the book and the true meaning of it. (Challoner)

St. John Chrysostom comments on 2 Timothy 3:16
2 Timothy 3:16, 17

All Scripture is given by inspiration of God, and is profitable for doctrine, for reproof, for correction, for instruction in righteousness: That the man of God may be perfect, thoroughly furnished unto all good works. [R.V.: Every Scripture inspired of God is also profitable, etc.]

Having offered much exhortation and consolation from other sources, he adds that which is more perfect, derived from the Scriptures; and he is reasonably full in offering consolation, because he has a great and sad thing to say. For if Elisha, ho was with his master to his last breath, when he saw him departing as it were in death, rent his garments for grief, what think you must this disciple suffer, so loving and so beloved, upon hearing that his master was about to die, and that he could not enjoy his company when he was near his death, which is above all things apt to be distressing? For we are less grateful for the past time, when we have been deprived of the more recent intercourse of those who are departed. For this reason when he had previously offered much consolation, he then discourses concerning his own death: and this in no ordinary way, but in words adapted to comfort him and fill him with joy; so as to have it considered as a sacrifice rather than a death; a migration, as in fact it was, and a removal to a better state. For I am now ready to be offered up 2 Timothy 4:6, he says. For this reason he writes: All Scripture is given by inspiration of God, and is profitable for doctrine, for reproof, for correction, for instruction in righteousness. All what Scripture? All that sacred writing, he means, of which I was speaking. This is said of what he was discoursing of; about which he said, From a child you have known the holy Scriptures. All such, then, is given by inspiration of God; therefore, he means, do not doubt; and it is profitable for doctrine, for reproof, for correction, for instruction in righteousness: that the man of God may be perfect, thoroughly furnished unto all good works.

For doctrine. For thence we shall know, whether we ought to learn or to be ignorant of anything. And thence we may disprove what is false, thence we may be corrected and brought to a right mind, may be comforted and consoled, and if anything is deficient, we may have it added to us.

That the man of God may be perfect. For this is the exhortation of the Scripture given, that the man of God may be rendered perfect by it; without this therefore he cannot be perfect. You have the Scriptures, he says, in place of me. If you would learn anything, you may learn it from them. And if he thus wrote to Timothy, who was filled with the Spirit, how much more to us!