The protagonist tends to be the "good guy," the one we root for and really like. Sula doesn't always fulfill this role, but she is the main character, and she serves as the link between the rest of the characters in the novel. Most of us probably do start to feel sympathy for her at some point, and maybe even like her.
Nel is the more traditional protagonist in the sense that she is the "good guy" for most of the novel. She is the one who is wronged by her friend and her husband, and she is the one we probably most identify with.