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Snape has every reason to suspect Lupin in PoA
Every so often, I'm reminded of the sheer number of fans who, upon re-reading PoA, cannot or will not attempt to understand Snape's perspective. They see his animosity towards Lupin as "pettiness", "prejudice", and "bitterness", and while of course he harbors all of the above to varying degrees, that's not the main driver of his behavior towards Lupin throughout the book? And his attitude, which is primarily one of suspicion, is anything but unwarranted.
Snape and Lupin's fraught history sometimes obscures the fact that in PoA, Snape also strongly believes Lupin is plotting with his old friend, the traitor and escaped mass murderer Sirius Black, to kill Harry. Snape says this explicitly, yet many fans seem to forget this when they interpret his behavior, instead painting Snape as irrational, unreasonable, or even maliciously spreading a lie about Sirius and Lupin so as to ensure their imprisonment. But you know what? He's got some pretty solid reasons to believe what he does.
Let’s follow his thinking here:
1. Sirius is a dangerous criminal who is headed to Hogwarts to kill Harry. Lupin, who will now also be at Hogwarts, may help his old friend target Harry.
Sirius Black–traitor to the Order, the Potters, and (oh yeah) a mass murderer–has broken out of prison for the purpose of killing Harry Potter. Everyone from the Minister to Dumbledore to Mr. Weasley is convinced of this. Snape, who never knew the identity of the mole in the Order, and who has his own history of being targeted by Sirius, has no reason to doubt this.
From Snape's perspective, it seems likely that Sirius will attempt to re-establish contact with his old friend, now in a position of authority at Hogwarts, to plan his attack on Potter. Lupin has never stopped Sirius from attacking before, why would he start now?
Snape warns Dumbledore about the possibility of Lupin helping Sirius get into the castle prior to the start of term.
2. Lupin attempts to gain Harry’s trust.
Lupin tries hard (a bit too hard?) to portray himself as a cool, approachable teacher. Snape seethes over Lupin’s attempts to butter up the Gryffindors at his expense; not only is it a severe reminder of his past bullying, but Snape could also see this as a machination on Lupin’s part to appeal to Potter. This approach would have worked with James, and Snape is convinced that Harry is just like him.
Then, Snape walks in on a private meeting between Lupin and Harry, taking place while all the other students are away. Lupin quickly (and obviously, to a spy and legilimens) changes the subject upon Snape’s arrival. Snape is suspicious; what is he up to? From Snape’s perspective, Lupin might be manipulating Harry, perhaps laying the groundwork to lure him into Sirius’s hands.
Furthermore, Lupin has a lax attitude about taking the potion. He won’t take it in front of Snape… would he perhaps "forget" to take it entirely? Is Lupin engineering a situation that will endanger Harry? Maybe Sirius intends to use his friend to kill the young student. Wouldn’t be the first time, would it?
Snape warily watches Lupin the rest of the night.
3. Only a few months into Lupin’s tenure, Sirius is able to evade security measures and get into the castle.
Is it a coincidence that this was the same day Lupin was paying special attention to Harry, and on a night very near a full moon? Snape thinks not, and reminds Dumbledore of the warning he gave him prior to the start of term. In Snape's mind, it's clear he was right to be concerned. When Dumbledore shuts his suspicions down, Snape knows that he must take matters into his own hands.
4. Lupin both passively and actively undermines security over the next few months. During this time, Black breaks into the castle a second time.
To Snape, Lupin’s avoidance of werewolves in class may indicate not simply self-preservation, but nefarious intentions. If Lupin were tasked with delivering Harry to Sirius, he wouldn’t want to jeopardize Harry’s trust by revealing his lycanthropy. And if the plot involved Lupin’s werewolf form, Lupin would need Harry to be ignorant so that he would be easy prey. Snape takes over teaching DADA for one lesson, intending to arm Harry (or his more talented friends, who can help look out for him) with knowledge of werewolves. His assignment on recognizing and killing werewolves reflects his suspicions and his high level of concern about the danger Lupin poses. He is not simply trolling Lupin here; Snape asked for the essays to be handed in to him, not to Lupin. Lupin’s cancellation of the assignment would serve only to further cement Snape's belief that Lupin is attempting to undermine student safety.
After a second breach of Hogwarts security and another failed attempt on Harry's life by Black, Harry is caught sneaking outside the castle on a Hogsmeade weekend. Snape is upset with Harry’s arrogance in playing fast and loose with his life, particularly in the present climate. When he interrogates him, he discovers the Marauders Map. As the parchment begins taunting him with familiar nicknames, the subject of his attention shifts from Harry to Lupin. He snaps into investigative mode--this might not just be Potter being an arrogant dunderhead, but another attempt by Lupin and Black to get Harry out of the castle. Furthermore, he was found right outside the Shrieking Shack, where Lupin and Sirius once almost killed another student. To Snape, the picture is coming together. When he confronts Lupin, Lupin flat-out lies to him and takes the suspicious parchment out of his possession. Lupin is undermining the protections around Harry and is working against Snape’s efforts to keep Harry safe, assuring Snape that he is guilty.
5. The grand plan finally comes to fruition. Snape, in the course of taking wolfsbane to Lupin after he has forgotten to take it, sees Lupin headed for the Shrieking Shack on the map Lupin supposedly knew nothing about. Snape now believes that Lupin has intentionally avoided taking the potion and that the plot he suspected was being hatched is now coming to fruition. It’s go time.
With an understanding of Snape's perspective headed into the Shrieking Shack scene, the question becomes: why should Snape listen to Lupin’s protests and hear him out in the shack instead of taking control of the situation and delivering these obvious criminals to justice? We understand his desire to head off, intimidate, threaten and thwart Quirrell in the Philosopher's Stone, so why, when he acts similarly towards Lupin, is it suddenly unreasonable? To Snape, what’s the difference between Lupin's protests in the shack and Quirrell’s in the forbidden forest two years previously?
At this point, Snape is assured Lupin is guilty, is frustrated with being brushed off this entire year, is faced with his bullies at the site of a huge trauma for him, is seemingly facing the exact same situation, and has just heard his tormentors discuss the event with absolutely no remorse. All that, of course, on top of the fact that he wholeheartedly believes Sirius was the mole in the Order and that Sirius is, at this point, the only other person he can blame for Lily’s death. Snape is extremely emotional and on edge during this confrontation--he lashes out, shrieks, snarls, calls Hermione stupid, and in general doesn't do himself any favors in the getting people to believe him department. But the belief he holds, that Lupin and Sirius are dangerous to Harry and the kids, is genuinely held and more than reasonable, given the information he is working with.
I consider your 4th point to be a bit of a stretch: no matter whether Lupin is having nefarious intentions or not, it makes perfect sense that he'd want to keep his secret. Agreed with the rest, however. And the fact is, Lupin was, in fact, covering for Sirius! At no point did he mention that Sirius, as an Animagus, would be able to bypass Hogwarts protections. The only reason things didn't turn out worse is because Sirius was innocent, which Lupin did not know at the time.
There is an oneshot, I don't remember the title, where Harry confronts Snape about the Lupin debacle in the aftermath, unhappy about Snape outing Lupin's secret. Snape makes this vary point. While Harry isn't really happy with Snape over the entire thing in the end, he is forced to concede Snape's point.
Prisoner of Azkaban is very interesting from Snape’s perspective. He was traumatized by what happened to him at the shrieking shack as a child and his belief that Lupin and Sirius were working together to harm Harry is validated by Hermione herself who came to the same logical conclusion. He was also unconscious when Sirius was revealed as innocent and so his insanity later with Fudge almost feels justified in a sense. A lot of Snape’s general unfairness in this book seems more reasonable when you remember how afraid he was of Sirius Black (someone he believes already tried to kill him once in his school days) and how desperate he was to protect Harry.
His behavior towards Neville was always awful but when the boy loses those passwords which prompts Black’s entry into the dormitory it almost makes sense how Snape punishes him for it later in the book. And even when Harry snuck out into Hogsmeade, of course Snape was livid about that. Lupin was, too.
Anyway, I really like this post.
