Here's how I've reasoned it out:
The requirement to honor and cherish goes in both directions. A child who fails to properly honor a parent can be forgiven and taught, since they are immature and not fully formed. A parent who mistreats and abuses a child may also be immature and not fully formed, but they are also responsible for deliberately and seriously damaging a growing human being.
Parenthood has two components: physical and emotional. Physical parenthood involved conceiving, giving birth, changing diapers, feeding, bathing, providing clothing, medical care, shelter. Emotional parenthood involves loving, caring, teaching, nurturing, correcting, protecting, encouraging, admonishing, supporting, releasing.
I have learned to accept that someone can be a parent in the physical sense but not in the emotional sense, some parents can parent well in the emotional sense but not, attimes, in the physical sense [job loss, catastrophe - 'you have to stay with Grandma for awhile, mommy has to work in another state, there are no jobs here and I want you to finish school where you are']. Others parent well in neither sense, and some parent well in both senses.
They are all parents, but by no stretch of the imagination are they all equal.
Again, I consider the admonition to honor a parent is matched and balanced by the admonition to properly care for and raise one's children. If my parent sees no reason to care for me or treat me lovingly, they have told me where I stand. Accepting that, and reacting appropriately to it, DOES honor them, because it respects their choice.