Even though we spend a little more time seeing things from Rahel's perspective, we really can't think about one of them as the protagonist without the other. Even in Rahel's mind, the two of them are a unit:
In those early amorphous years when memory had only just begun, when life was full of Beginnings and no Ends, and Everything was Forever, Esthappen and Rahel thought of themselves together as Me, and separately, individually, as We or Us. As though they were a rare breed of Siamese twins, physically separate, but with joint identities. (1.9)
While we see things from a number of different characters' perspectives, this novel is undeniably about the twins. They are the two people we feel scared for, that we smile at, and that we question. They're the ones we cheer for in good moments and want to hug when things don't go well.