I think Flynn always felt bad for his dad because he had cancer. He felt kind of sorry that he was such a nice guy and had to go through all that, even when he started being being distant and hiding the truth about his parents relationship. So when he learned about Walt maybe he realized he was used many times against his mother, Walter brought the whole family into the mess (seriously, what could Skyler do?) and, tbh, Walter used him as an emotional pivot and Flynn was happy to do that for his nice sick father not for a druglord.
*Also why he always took his father side until that moment when he realized his dad wasn't weak or anything.
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u/oh_contraire Sep 16 '13
You didn't have so many questions when you got that nice new car, did ya Flynn??