Introduction
There are significant difficulties harmonizing the Reformed doctrine of the perseverance of the saints with the teaching of the epistle to the Hebrews (as well as other passages of Scripture), and these difficulties show it to be an unbiblical doctrine. The Reformed generally (though not, perhaps, all of them) hold as an article of faith that the “Elect” cannot lose their salvation:
I. They, whom God has accepted in His Beloved, effectually called, and sanctified by His Spirit, can neither totally nor finally fall away from the state of grace, but shall certainly persevere therein to the end, and be eternally saved.
II. This perseverance of the saints depends not upon their own free will, but upon the immutability of the decree of election, flowing from the free and unchangeable love of God the Father; upon the efficacy of the merit and intercession of Jesus Christ, the abiding of the Spirit, and of the seed of God within them, and the nature of the covenant of grace: from all which arises also the certainty and infallibility thereof. [WCF 17.1, 2; the source includes links to passages advanced in defense of the doctrine]
At least some Reformed may not hold the doctrine in exactly this way, but the majority of conservative, orthodox Presbyterians do so. There are significant difficulties making this doctrine “fit” what is taught in the epistle to the Hebrews and other New Testament books. The fact that the doctrine cannot reasonably be said to fit the teaching of Hebrews (and other books) strongly indicates that it is an unbiblical doctrine.
Hebrews 3
Therefore, holy brethren, who share in a heavenly call, consider Jesus, the apostle and high priest of our confession. … Take care, brethren, lest there be in any of you an evil, unbelieving heart, leading you to fall away from the living God. [verses 1, 12]
In this passage, the author of Hebrews calls his audience “holy brethren,” and says they “share in a heavenly call.” And then he warns them against unbelief. This does not support the Reformed doctrine of perseverance. A heavenly call does not reasonably seem to be something different from the effectual call referred to in the WCF, and the identity of the two seems all the more certain in that the author calls them holy brethren. Yet he also deems it necessary to warn them against falling away from God and being found with an evil, unbelieving heart. If the Reformed doctrine of perseverance were true, such warnings would be both absurd and unnecessary: the author clearly understands his audience to be among the elect, and so a warning like this would be irrelevant.
Hebrews 6
For it is impossible to restore again to repentance those who have once been enlightened, who have tasted the heavenly gift, and have become partakers of the Holy Spirit, and have tasted the goodness of the word of God and the powers of the age to come, if they then commit apostasy, since they crucify the Son of God on their own account and hold him up to contempt.” [verses 4-6]
According to the Reformed, the non-elect never become partakers of the Holy Spirit precisely because they aren’t chosen by God (see here). This contradicts what the author of Hebrews says in this passage: he says that apostasy is a danger for the elect, because there are people who have partaken of the Holy Spirit who may indeed commit apostasy.
Hebrews 10
For if we sin deliberately after receiving the knowledge of the truth, there no longer remains a sacrifice for sins, but a fearful prospect of judgment, and a fury of fire which will consume the adversaries. A man who has violated the law of Moses dies without mercy at the testimony of two or three witnesses. How much worse punishment do you think will be deserved by the man who has spurned the Son of God, and profaned the blood of the covenant by which he was sanctified, and outraged the Spirit of grace? [verses 26-29]
According to the Reformed, the only people who are sanctified by the blood of the covenant are the elect. This passage says that there is a man who has profaned the blood of the covenant by which he was sanctified. This implies that he is elect. The rest of the passage makes clear that an elect man who sins in the way described loses his salvation. This passage does not support the Reformed doctrine of perseverance, because that doctrine does not allow for the possibility that the elect may fall away (as is clearly taught here in Hebrews).
Hebrews 12
See that you do not refuse him who is speaking. For if they did not escape when they refused him who warned them on earth, much less shall we escape if we reject him who warns from heaven. [verse 25]
According to the Reformed, the elect will never reject God. This passage warns of the dire consequences for “us” (first person plural, including himself) if we reject God. This means either that the author of this inspired book of the Bible did not consider or know himself to be elect (which seems absurd on its face, and by itself seems to undermine the Reformed doctrine of perseverance) or that the elect can in fact lose their salvation. This passage does not support the Reformed doctrine either.
Aside from Hebrews, though, there are other passages in Scripture which similarly undermine the Reformed doctrine of perseverance.
Deuteronomy 7
For you are a people holy to the Lord your God; the Lord your God has chosen you to be a people for his own possession, out of all the peoples that are on the face of the earth. [verse 6]
What this passage says is that Israel was chosen by God. But what else is it to be “elect” than to be chosen by God? There is no difference; the two expressions mean the same thing. If we allow Scripture to interpret Scripture (as Protestants insist), it seems pretty clear that this verse has something important to add to our understanding of what it means to be elect. Why? Because large numbers of Israelites fell away. Hence the possibility of apostasy is perfectly in keeping with what the Bible says about election (as an aside, the fact that Deuteronomy 28:15-68 presents a terrifying catalog of the consequences of apostasy for these people who are elect ought to remove any doubt about the fact).
1 Corinthians 9
I pommel my body and subdue it, lest after preaching to others I myself should be disqualified. [verse 27]
If anyone on earth could know he is elect, it was St. Paul. Yet he says he labors to avoid being disqualified. The Apostle is unwilling even to take his own redemption for granted, and realizes that even he could fall away. There is no other sensible way to interpret this passage.
2 Peter 2
For if, after they have escaped the defilements of the world through the knowledge of our Lord and Savior Jesus Christ, they are again entangled in them and overpowered, the last state has become worse for them than the first.” [verse 20]
The Reformed deny that non-elect people have any knowledge of God, citing Romans 1:18 & 3:11. more significantly for our purposes St. Peter strongly implies that the people in question here have enjoyed some measure of sanctification. This, say the Reformed, is impossible. The Prince of the apostles goes on to say that people who do know Christ may become defiled by the world again and that their last state is worse than their first (before they were Christians). This implies they can lose salvation: if they were not elect, then “falling away” (so called) would leave them in the exact same state they had always been in and it would be impossible for their last state to become worse.
Objections
To be fair, it isn’t as though the Reformed are completely ignorant of these passages (although in my experience these verses receive very, very little attention among them). And of course they attempt to harmonize these passages with their doctrine and would deny that these passages disprove their view.
The problem with these efforts, it seems to me, is that they are founded upon the question-begging premise that the Reformed view is correct. But that is precisely what is in dispute. Furthermore, their arguments do not take sufficient account of the evidence of Deuteronomy 7, which unambiguously demonstrates that the Elect can and do sometimes fall away, losing their salvation. Alternatively the Reformed argue that by their principle of letting Scripture interpret Scripture, their view is assured. This too is question-begging: which passages of which books should be the plumb line? It is ridiculous to say that the “clear” passages should be the guide for the “unclear” ones’ interpretation, for who is to say what is clear or unclear?
A second line of defense is grounded in the decrees and/or providence of God. I have even occasionally heard Aquinas’ name bandied about in this regard, claiming that this was his view. Well, yes and no. Yes, he affirms the certainty of divine providence, but he also insists that providence takes the nature of things into account: contingent events happen contingently. Man has free will, and God does not overthrow that gift; rather, His providence ensures that His will is done in and through the free choices of men. We are not compelled. And this being the case, Aquinas simply did not hold to any view of God’s sovereignty that reduces to fatalism. On the other hand there is no rational way for the Reformed to escape the charge of fatalism precisely because they deny that we have any choice in the matter of our salvation.
Conclusion
The Presbyterian/Reformed doctrine of the Perseverance of the Saints crumbles under the weight of far too many passages of the Bible that simply cannot be interpreted in harmony with that doctrine. Their explanations of these passages beg the question of their view’s legitimacy, rather than allowing their doctrine to be formed by the text.
Aquinas, Etc. 
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