Madoka and Homura represent two extremes of love. The conflict between them stems from the difference between the inclusiveness of Madoka’s love and the exclusiveness of Homura’s love.
As we meet Madoka for the first time, we also meet her family and friends. We find that the world that Madoka grew up in is full of support and togetherness. She is part of a loving family and of deep friendships. This is what allows Madoka to sacrifice herself at the end of the series. Madoka takes the sacrifice of resigning herself to provide for the well being of others, because she truly feels that the world is a place of inclusion and togetherness. She’s capable of doing this because for her, it isn’t a kind of resignation — alleviating others’ suffering alleviates her own suffering. Everyone is included as part of a whole. As she saves others, she also saves herself.
Homura, in contrast, never had the support and togetherness of Madoka’s upbringing. For all her life, she has been alone, and this shapes her into a character with a single-minded, exclusive form of love. At the same time that Madoka reaches out and includes Homura into her circle, Homura is doing the opposite: once she attaches her affection to Madoka, she excludes everyone but Madoka from her consideration. The world means nothing to Homura, because she’s never meant anything in the world. This is why at the end of Rebellion, she sacrifices all of the world to ‘save’ Madoka from resigning herself.
The two’s actions are incomprehensible to one another. Madoka’s love is selfless and includes everyone, whereas Homura’s love is selfish and excludes all but Madoka.