There was little ambiguity about that. The only time that it was ever in question was in S1, but after the "chuck was behind it" reveal, it was clear that he wasn't a bad guy.
He made several gestures in good faith to both Jimmy and Kim, which made their plot to destroy him absolutely baffling.
The entire time I was yelling, "WHY? JUST WHY?". Neither at that point had a compelling reason to hate him. Heck, he made active attempts to mend fences before Jimmy and Kim went after him.
Also, Kim should've went to prison. Not just sued.