Joe feels that Bob was a bad father because he didn't let him pursue a career solely based on music. Also, most teenagers think their parent(s) are bad ;)
In my opinion, Bob was the best father he could be. He lacked connection with Joe, but he did put the effort in...having him come to the boat house, allowing Cal to always hang out, attending the basketball game, teaching him about nature/hiking, etc. I think Ingrid would agree that Bob was a decent dad.
If Bob was still alive after Joe and October hooked up at the end, I think "the new Joe" would have worked on creating a new (more appreciative) relationship with Bob.