Who are the “protagonists”?

Although, strictly speaking, a literary work can have only one protagonist, it would be hard to pick one of the three young men over the other two for that role. So I'd have to say it's all three of them. And the antagonist must be Death. The conflict starts as one between them and Death but turns into one between the man who goes to buy provisions and the two who remain behind.

The theme as the Pardoner himself announces it is "Radix malorum est cupiditas"--"Greed is the root of evil." The story certainly illustrates that point, but we might also see it as the "no honor among thieves" theme.

The setting, again as the Pardoner explicitly states, is Flanders (present-day Belgium, just across the Channel from England) during the Plague. THE Plague struck England in 1348-1349 (when Chaucer was a child), and there was another outbreak about twenty years later. In other words, the tale takes place not very long ago for the pilgrims and in a familiar place not very far away.

Since the Pardoner makes his living by selling indulgences (pardons), he must generate a need for his wares by making people aware of their sins. So he preaches about sins, and this sermon is on the theme or text mentioned in the second paragraph. The sin is greed, which as he describes it includes both gluttony (and drunkenness) and avarice. In the story, greed for food and drink causes the three friends to split up, and greed for bigger shares of the gold they have found leads them to betray and kill one another. The moral of the story is fairly obvious, but then we have to fit it into the context of the Pardoner himself. No doubt he convinces his usual audience of their own sins and their need for pardon, but he has already told the Canterbury pilgrims how he operates, so that when he concludes his presentation by urging his hearers to buy his pardons, he's like a magician who has shown his audience how a trick works. Then of course there's the fact that he is telling this story to make money, so that he's guilty of the very sin he preaches against.

Although, strictly speaking, a literary work can have only one protagonist, it would be hard to pick one of the three young men over the other two for that role. So I'd have to say it's all three of them. And the antagonist must be Death. The conflict starts as one between them and Death but turns into one between the man who goes to buy provisions and the two who remain behind.