I think that it is natural and healthy for a child to recognize that his/her parents are not perfect, as Rebbetzin Heller said in the shiur, the point of using Dama ben Netina as the example of Honoring parents is because he honored his parent solely because they gave him the gift of life, not because they were necessarilly great people who he highly repected.
Nowadays it is so hard to engender respect for parents while ensuring the children feel a relationship of love and warmth. But the truth is that it is possible to accomplish this. We can give lots of love while still insisting on boundaries.
I think it is a good idea to introduce certain practices into the home, to train children to treat parents with the respect prescribed by the Torah. Having children rise for you once in a while, or insiting that a certain chair be special for Abba, will introduce the concept of respectful actions. This wil eventually lead to true respect.
This recently came up in my family. My husband sometimes 'rough-houses' with my two sons, aged 5 and 8. For him, it is a way of showing affection and positive interaction (I don't really get it, but apparently it's a male bonding type of thing

). Then one of my kids responded a little too roughly, and I suddenly realized that we were training them to act disrespectfully. He's not their uncle he's their father! They can have bonding activities, they can play, read learn, have fun together, but there must always be a clear boundary between friend and father.