This is a question typically asked in a moral critique of a literary work, but in this situation it is not easily answered. In a typical story the protagonist, or hero, has good morals and good intentions, while the antagonist, anti-hero, has bad intentions with morals that most would agree are detestable. In the end the hero is rewarded and the bad guy is punished, effectively teaching the reader, of any age, the simple lesson that being good is the way to go in life because there are less consequences.
In Frankenstein, it is much more complicated and requires more thinking and critical analyzation than say: a Disney princess movie. I think that most would agree that fairy tales are not the most realistic representation of human nature, and that is the major difference in terms of the effectiveness of Frankenstein. Victor is neither good, nor bad; he is simply human: a being, like most animals, who displays both qualities at different times depending on multiple different things. This source of morality is one of the major truths behind the novel and it can be argued from multiple points of view.
Some would view Victor as the protagonist throughout the story, for he is the main character; but others would view his helpless creation as the "good guy" - even though the creature performs acts which most would agree are repugnant. Picking sides on this issue is a waste of time and it shrouds our judgement from seeing the true picture. Neither of the characters can be classified as the protagonist or the antagonist because it is possible to justify both of their actions in logical and emotional and reasonable ways. Because they are both examples of human nature taken to the extreme, or simply what could happen to any of us, both of their lives and the story ends. It is unclear whether the characters see this death as a reward or punishment, but to the readers it is clear. With death being the ultimate fear of human beings, it is no wonder that Shelley chose to end her story in this way, to use this fear as a warning to fight against human nature and to keep morals alive by learning from others' mistakes.