The protagonist of Mary Shelley's novel Frankenstein can be confusing given the use of the multiple narrative voice seen in the novel. For some, the main speaker of any given work is seen as the protagonist. In this case, Walton would be considered the protagonist (given he is telling Victor's tale).
That said, some may argue that Victor is the protagonist of the novel. The story encompasses Victor's life, loves, and conflicts. The story would not exist if it were not for Victor's experimentation with reanimating life and his success at doing so.
Others may believe that the Creature is the protagonist. This can come about given some readers may feel sympathy for the abandoned "son" of Victor.
Essentially, an individual reader could successfully justify the protagonist of the novel as any of the three "main" characters of the novel. With each declaration of the protagonist, the antagonist changes. If Walton is defined as the protagonist, the antagonists are nature (external conflict) and himself (internal conflict). If Victor is deemed the protagonist, both the Creature (external conflict) and himself (internal conflict) would be the antagonists. If the Creature is deemed the protagonist, Victor (external conflict), society/mankind (external conflict) and himself (internal conflict) could be considered his antagonists.
I would argue that the Creation is the Protagonist; we enjoy his perspective more, and he is the focus of the novel. We follow his actions and voice most, and when not, we follow his actions through other characters.
While the term Protgonist is not defined as the "good guy," I find myself siding with the Creation because of this.
Chapter Twelve (about two pages in) The monster recalls his story, specifically about his time spent with the villagers. He proves himself to be kind when he says "...but when I found that in doing this I inflicted pain on the cottagers, I abstained and satisfied myself with berries, nuts, and roots..." Where he had previously stole from them to survive, the pain he caused told him to gather other food from the wood to alleviate the peoples' pain.
We "side" with him as he vows revenge and kills William; there are even parts of us in chapter 16 that feel a strong connection to him. He has been wronged, and William has it coming to him.
We pity and empathize with him in chapter 19 when he works in isolation; this is contrasted with the pity we cannot feel for Frankenstein as a doctor. Frankenstein chose to isolate people by being a scientist in his line of work; the Creature WANTS to be accepted, and consistently reaches out to people, only to be rejected. He is even rejected by Frankenstein at the moment of his own "birth" (which is in Chapter 5 in Frankenstein's point of view, and described further in chapter 20).
I would stress that the creation is one we pity and almost love. We understand that his crimes are only those he feels are deserved, or MUST be done; we smile at his vegetarian diet, and we reach out for him and are willing, as readers to do what the characters in the novel cannot: treat him as a human being.