I think the main reason is the way a good story is designed. There are the good guys and the bad guys-- there is the conflict and the resolution. It makes for a better story (thanks to Cinderella) Someone has to be the bad guy.
Being a step parent myself- I know how much I have poured into my step children and still will never have the place in their heart that I wish I could. It is wonderful to be "mom"- it is hard to be called "my dad's wife" after 20-plus-years of caring for them while their "real" mom was too busy with drugs, parties, and other distractions. You have to love them.
Oh well- what do you do? I say write new stories :)