I think that Anne holds more sympathy and loyalty to her father than to her mother. It seems to me that the relationship between Anne and her mother is representative of a typical adolescent relationship. This becomes very distinctive when looking at the time period in which the diary takes place. Adolescence is present, even in the most inhuman of times. Anne's spirit of independent identity comes into conflict with her mother's traditionalist view of what it means to be both a woman and a child. This conflict is where Anne views her mother differently. I think that there is a more tolerant view of her father presented, but she does feel that both of them do not have a full grasp of the emerging identity that Anne undergoes throughout the course of her diary entries.
Before going into hiding, Anne viewed her parents as any adolescent does; those caregivers that provide the essential things I need to survive. Perhaps Anne also considered the authority that her parents represented in her life as well.
Once they were in hiding, however, Anne sees her parents in their unguarded rawness. They are simply human. There are no bedroom doors to have private discussions behind, there is no workday to tout your sustaining effort on, and the mists of romantic relations are forever repressed by the lack of dignified privacy. Anne glimpses moments of vulnerability in her mother and father - who have always been the protectors of her world before the Nazi's. She struggles with the role her parents fulfilled outside of hiding, and what slim semblence of family is left to them in their precarious situation.
Putting it more plainly, Anne never truely thought of her parents as "human" before. She's seeing that this situation they are in isn't at all like home. She comments that her mother is always cross with her and that her father is forever more patient. Some would say that she is simply a self-centered brat who can only think of herself; being drawn to the parent that treats her the "best" is natural for someone her age. However, in other parts of the text, one can find examples of Anne's generosity and sharing that would show Anne's ability to think outside of her own needs and selfishness.
As Anne's diary grows in length, so does her understanding of her parents as individuals seperate of their relationships and roles.