I thought it was kind of weird how Flynn turned on Walt so fast. At first Flynn is listening to Walt, completely dismisses the drug story that Skylar told him and then Flynn even almost obeyed Walt to go pack.
Then Flynn sees Skylar use the knife on Walt and then Walt tries to get the knife away from Skylar and all of a sudden Flynn gets protective of his mom and threatens Walt?
It made sense to me. He worshiped his dad. He had to see it and hear it from the horse's mouth to believe it, but the kid is the moral core of the show. He eventually got it. Even told his mom straight up, "You're a liar." No hesitation. If you ever want a cue whom to root for, follow Flynn's lead.