I honestly think that when most people say "our parents did the best they could", that they don't really mean it. Usually, no matter how much anger or resentment you have towards your parents, part of you still has this unconditional love for them. By saying they did the best they could, your trying to make them sound like they aren't "bad" people.
I never really thought about the expression.... but now that I am, it really is just an excuse (in most cases).