Even though we know from the start that Hannah is dead, we still empathize with her throughout the story. We might question her actions and even get angry with her, but she's the one we're rooting for (especially in a world full of super mean teenagers).
Clay is our living protagonist. He's a nice guy going through the roughest time of his life. He quickly gains our trust and sympathy; we feel bad about what he's going through and we want to see things get better for him. He maintains his good-guy status by actually changing in a positive way after listening to Hannah's tapes; he is able to self-reflect and use the tragedy to become a better person.