It was kind of surprising to see him react to the knife fight the way he did. I mean Skyler slashed at Walt. It seemed like Walt just tried to subdue her and get the weapon away, and Flynn now views that as his dad attacking and trying to hurt his mom? Wow. The kid's really been hurt to have switched over so quickly.
I didn't find it surprising at all. He's a decent kid and now he's got the facts he saw the situation the way it is: Walt's the bad guy.