An important note. This topic is surely filled with material that is horribly offensive. In the text below, I am trying to describe various beliefs which I do not personally hold, and to which my denomination (regrettably, only since 1986) no longer subscribes.
One Antichrist or many?
The cited passage from 1 John does indeed talk about many antichrists; it also mentions a unique "the antichrist" who is to come. Several other Biblical passages have been interpreted in support of the existence of a single figure; see for example St Jerome's commentary on Daniel. Augustine (City of God 20.19) similarly says:
As therefore there went out from the Church many heretics, whom John calls many antichrists, at that time prior to the end, and which John calls the last time, so in the end they shall go out who do not belong to Christ, but to that last Antichrist, and then he shall be revealed.
Robert Lerner (a historian of medieval heresies and millenarian movements) writes:
Yet, since the author of 1 John drew a distinction in this very passage between the "many antichrists" who existed "even now" and a great Antichrist who "shall come", patristic authorities and medieval theologians concluded that the "many antichrists" were any members of the diabolically inspired human society of evil, all of whom helped to prepare the way for the true Antichrist's coming, but none of whom were to be confused with the Antichrist himself. 1
So, before the Reformation, there was a long tradition of belief in a single future great enemy, whose coming would be anticipated by many lesser antichrists. In the passage you quote, "man of sin" and "son of perdition" are taken from 2 Thessalonians 2:3, which is another prophetic warning about someone usurping the position of Christ - typically identified with the same unique Antichrist.
Popes and the Papacy
Reformation and earlier opponents of the papacy commonly associated the current Pope, the institution, or both, with capital-A Antichrist. There are a few mutually-supporting reasons, though in some cases this is mere name-calling. One view is influenced by the prophetic idea of Antichrist: he is believed to be a future occupant of the See of Peter, and the Popes until then (keeping his seat warm) could be identified with him since they were all thought to be working towards the same diabolical goal. Less eschatologically, the Popes were seen as representative of an ongoing system of oppression; they could each be called Antichrist since they were its leaders.
Some examples (from 1 and 2 Thessalonians through the centuries, Anthony C Thiselton, Wiley 2010):
- Joachim of Fiore "is the first to associate [Antichrist] with a triumphal pope."
- John Wycliffe (of the Lollards) "was still more emphatic about identifying the Antichrist with the pope or the papacy, or even with institutional church wealth and power"
- John Huss "sees the Antichrist as the Pope himself as an individual man"
- Martin Luther "insisted that the Antichrist was the Papacy". See his Against the Execrable Bull of Antichrist, the reply to Leo X's bull of censure Exsurge Domine, in which he lashes out at those responsible for the letter, in pure invective. But his condemnation was less for the individual than for what he represented:
"Luther held that every Pope was Antichrist even though personally exemplary, because Antichrist is collective: an institution, the papacy, a system which corrupts the truth of Christ. That was why Luther could repeatedly address Leo X in terms of personal respect only a week or so after blasting him as Antichrist." 2
John Calvin also takes the institutional view, but with the Pope as representative of the corrupted universal church, therefore occupying "the seat of Antichrist" 3. Since the 1689 Baptist confession you cite is coming from the Calvinist tradition, this may be the most relevant line of interpretation. The key passage from the Institutes is 4.7.25:
To some we seem slanderous and petulant, when we call the Roman Pontiff Antichrist. But those who think so perceive not that they are bringing a charge of intemperance against Paul, after whom we speak, nay, in whose very words we speak. But lest any one object that Paul's words have a different meaning, and are wrested by us against the Roman Pontiff, I will briefly show that they can only be understood of the Papacy. Paul says that Antichrist would sit in the temple of God (2 Thess. 2:4). In another passage, the Spirit, portraying him in the person of Antiochus, says that his reign would be with great swelling words of vanity (Dan. 7:25). Hence we infer that his tyranny is more over souls than bodies, a tyranny set up in opposition to the spiritual kingdom of Christ. Then his nature is such, that he abolishes not the name either of Christ or the Church, but rather uses the name of Christ as a pretext, and lurks under the name of Church as under a mask. But though all the heresies and schisms which have existed from the beginning belong to the kingdom of Antichrist, yet when Paul foretells that defection will come, he by the description intimates that that seat of abomination will be erected, when a kind of universal defection comes upon the Church, though many members of the Church scattered up and down should continue in the true unity of the faith. But when he adds, that in his own time, the mystery of iniquity, which was afterwards to be openly manifested, had begun to work in secret, we thereby understand that this calamity was neither to be introduced by one man, nor to terminate in one man (see Calv. in 2 Thess. 2:3; Dan. 7:9). Moreover, when the mark by which he distinguishes Antichrist is, that he would rob God of his honour and take it to himself, he gives the leading feature which we ought to follow in searching out Antichrist; especially when pride of this description proceeds to the open devastation of the Church. Seeing then it is certain that the Roman Pontiff has impudently transferred to himself the most peculiar properties of God and Christ, there cannot be a doubt that he is the leader and standard-bearer of an impious and abominable kingdom. 3
Jacobus Arminius, citing 2 Thessalonians 2, similarly wrote (Disputation 21: On the Roman Pontiff):
The name of "The Antichrist" belongs to [the Pope] pre-eminently [...] for he is both a rival to Christ, and his adversary, when he boasts of himself as the spouse, the head, and the foundation of the church, endowed with plenitude of power; and yet he professes himself to be the vicegerent of Christ, and to perform his functions on earth, for the sake of his own private advantage, but to the manifest injury of the church of Christ.
1. Antichrists and Antichrist in Joachim of Fiore, Robert E. Lerner. Speculum 60:3, 1985.
2. Here I stand: A life of Martin Luther, Roland H. Bainton. Hendrickson Publishers 2009.
3. Institutes of the Christian Religion, John Calvin. Translated by Henry Beveridge.