The previous educators have classified this relationship as complex and complicated, and I think those are great descriptors. I would add that Dana's feelings toward Rufus are symbolic of the typically impossible situation slaves found themselves in.

Dana has every reason to hate Rufus. He is cruel, abusive, and vindictive. Yet Dana realizes that her own destiny is inextricably bound to his because he is her ancestor. Without going too much into timeline theories, it stands to reason that if Dana kills Rufus (or allows him to be killed) before he has children, she wipes herself out of existence. Many slaves found themselves in similar situations of impossibility with no hope of escape. Even if they organized a rebellion and killed their slave owners (which was done from time to time), they knew that a retribution would follow and they (and their families) would be killed.

Dana also struggles with Rufus's character. On one hand, she sees glimpses of goodness in him, and she holds out hope that she will eventually influence Rufus, helping him to be a better person. Yet Rufus is the only one with power, and he has always been so spoiled and coddled that he is ultimately a hopelessly selfish man. This type of relationship is represented historically, with slaves often trying to find glimpses of goodness and therefore hope in their owners. Frederick Douglass comments in his autobiography that his owner, Mrs. Auld, treated him with a "kind heart" and was thankful for her initial efforts in teaching him to read.

Dana symbolically represents the life of many slaves, whose feelings weren't easily definable and who endured impossible situations to survive day after day.

Dana and Rufus have an extremely complex relationship because when Dana travels into the past, she is a slave while Rufus is the plantation master, but she also later finds out that she is biologically related to Rufus. Dana's relationship with Rufus is typical of slave-master relations in many ways. 

Dana is an adult woman living in the 1970s when she is inexplicably transported to the antebellum South. As a black woman, she is automatically considered a slave in the past, even though she is a professional writer in her "real life" in 1976. While she is a slave on the plantation, she is mistreated and beaten, as the other slaves are. However, because of her historical knowledge and intermittent returns to the 1970s between trips to the past, she is better equipped to survive the hardships she must endure. Even though Rufus is very young when Dana first arrives, on later trips, he has grown up and become the master of the plantation. He can often be cruel, exerting the full force of his power. He rapes another female slave and even attempts to rape Dana. 

Also late in the novel, Dana discovers that Rufus is one of her ancestors. This obviously creates an inner conflict because Dana knows how flawed he is. Her situation, though, was very common during slavery. Masters often raped their female slaves and impregnated them. Therefore, many children were the products of the union of a slave and her master. Dana, living in the 1970s, is removed from the immediacy of this truth, but when she is thrust into the past, she must face it head-on. Despite the complexity of her feelings, Dana ends up killing Rufus, and she and her husband Kevin agree that Rufus's death is for the best. 

The relationship between Rufus and Dana is a highly complicated one, and at one stage the author draws a deliberate parallel between the way that Dana feels about him to the way that his slaves feel about him. Note how this is established in the following quote, taken from Part 11 of "The Storm":

They seemed to like [Rufus], hold him in contempt, and fear him all at the same time... I had thought my feelings were complicated because he and I had such a strange relationship. But then, slavery of any kind fostered strange relationships.

Dana is talking of an incident when Rufus handed out scraps of food and alcohol to his slaves round a campfire. She is struck by the way that the slaves overtly are grateful to him for these small gifts, but at the same time how they then insult him behind his back. The slaves, having lived as slaves for all their lives, find themselves naturally grateful to their master for the gifts that he gives them, even though at the same time they continue to hate him for keeping them as slaves. Dana finds similar contradictory feelings within her own relationship to Rufus, and is shocked to realise that she is not as different from the slaves as she had thought she was. The final sentence of the quote signals to the reader the profound wrongness of slavery: slavery fosters "strange relationships" because of how unnaturally wrong it is. Dana's relationship with Rufus is therefore characterised by both loathing and hatred, but also occasional moments of affection and gratitude.