The protagonist is the character who concerns the conflict, really. Otherwise that would mean that every deus ex machina-as-character that resolves a conflict is the protagonist, and that's clearly not the case. The protagonist is the person the conflict revolves around, and for who the audience identifies with. Madoka doesn't fit this description because she's, in a sense, the 'prize' that everyone plays around, being the goal of Homura and Kyubey and such. Homura fills the position because her struggles cause the series to happen, and it is her devotion to suffer hell to save a loved one that we are expected to empathize with.
Madoka would be a deuteragonist.
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