Mom is descended from fallen nobility, but has a commoner appearance. The sis several of the traits from their noble ancestors and as such has a "noble" appearance. MC looks like her parents and acts slightly differently from everyone else (which makes sense since God would not favor a random idiot hick who is 100% like all other idiot hicks. she needs to be purer then the rest) which lead to she is different so treat her worse started by the father.
Heck, from the first WN chapter, she was being abused by the entire village but constantly protected by convenient coincidences as since she is the Miko nature was protecting her.