The question now is: how does identifying the Papacy with the antichrist fit in here? The obvious answer is that since Rome's Gospel was radically corrupt in the eyes of the (Pretend) Reformers, this could only mean Rome was (logically) some massive puppet of Satan. Where Dr Anders leaves off though is where I'd like to focus on, which is the question of whether this identification is an "essential" Christian teaching, plainly taught in Scripture.
As Dr Anders points out, there is a modern trend to drop references to the Antichrist out of historic Confessions, such as what the (conservative) Presbyterian Church in America has done in adopting the 1789 American revision of the original (1646) Westminster Confession of Faith (see Their Statement). The Orthodox Presbyterian Church adopted this revision as well. More and more "conservative" Protestants today are backing off from this identification, even going so far as to say Rome isn't even apostate.
Folks like TurretinFan stand behind the original Westminster Confession, holding the Pope to be the Antichrist. But this raises the question: which version of the Confession is right? To identify someone as the Antichrist is no small charge; it's not something that can be simply excused as a matter of personal preference. Which of the two is engaging in proper exegesis? The 1646 WCF gives this as the "Scriptural Proof" for identifying the Pope with the Antichrist:
2 Thess 2:3 Let no man deceive you by any means: for that day shall not come, except there come a falling away first, and that man of sin be revealed, the son of perdition; 4 Who opposeth and exalteth himself above all that is called God, or that is worshipped; so that he as God sitteth in the temple of God, shewing himself that he is God. 8 And then shall that Wicked be revealed, whom the Lord shall consume with the spirit of his mouth, and shall destroy with the brightness of his coming: 9 Even him, whose coming is after the working of Satan with all power and signs and lying wonders.
Rev 13:6 And he opened his mouth in blasphemy against God, to blaspheme his name, and his tabernacle, and them that dwell in heaven.Exegetically, it seems the identification is quite weak. First of all, as Dr Anders noted, the context of these passages is apocalyptic, yet as the centuries go by this seems less and less plausible given that the end of the world still hasn't happened. In other words, it was easy for someone like Luther to make this charge, since he thought the end of the world was near, but his predictions have gone the way of the Millerites and Harold Camping. Second of all, and credit for this goes to someone in TF's comment box, the text speaks of this Antichrist coming from inside the true church, which is impossible if Rome never was a true church. This would entail the ultra absurd historical proposition that there were two parallel visible churches, which diverged at the Reformation. Thirdly, the term "Antichrist" doesn't even appear in these texts. The term "Antichrist" does appear in the Bible (only in St John's Epistles: 1 John 2:18-23; 1 John 4:3; 2 John 1:7), but I suspect the reason why these texts were not referenced was because they identify the Antichrist with denying Jesus has come in the flesh and is the Messiah (i.e. the core Christian dogma). This cannot be charged of Catholicism because Catholicism affirms this core Christian dogma. [UPDATE: I would add another detail that someone showed me, which is that the "Man of Sin" seems to refer to a single individual, not an office or succession of people.]
So when all the evidence and reasoning behind identifying the Papacy with the Antichrist is considered, it becomes clear this was a fatal blunder on the Protestant end. What we have here is essentially an old fashion case of false prophecy, akin to the false prediction as the Jehovah's Witnesses. The JWs claimed 1914 marked the start of the "last days," meaning Jesus would return any moment within a "generation," and since the JWs "rightly" predicted this, it means they're the true religion. Yet as we near the century mark this is becoming a self-refuting prophecy. Similarly, the Pretend Reformers based their entire motivation for tearing apart the Church on the basis of (falsely) prophesying that we were in the end times and that the Pope was the Antichrist. Given that the Papacy is still here 500 years later, and Protestantism is heading out the door, we see the Reformers were wrong. They were right to recognize that for the Papacy to be such a powerful position that he is either propped up by God or from Satan, but unfortunately they placed all their bets on the wrong side of the table.
As noted earlier, this embarrassment has led to the dropping of the reference by some modern Protestants, but I believe this turns it into a matter of revisionist history. If the original identification was wrong, then this has huge implications for the credibility of the first Protestants. So the modern day Protestant is stuck: either they admit the first Protestants were very wrong, or they cling to laughable exegesis and pretend that this is acceptable.