This show definitely has it's dark undertones. There is no denying it, but that doesn't necessarily make it bad, does it? Some of you may remember "Aaah Real Monsters!", "Courage the Cowardly Dog", and "The Grim Adventures of Billy and Mandy". If you can recall, they all had their fair share of creepy, scary moments, but as far as I know, they didn't do any harm. Why should "Flapjack"?
I realize, the characters are not the best role models in the world, but that's what's so great about this show--it's a good dose of reality. The characters aren't the typical "bad role model characters". They actually have a great deal of depth for a children's cartoon. Bubby, Flapjack's adoptive mother, while being an eavesdropper and frequently hypocritical, she just wants the best for her son and will go to great lengths to ensure his safety and always has his best-interest at heart, even though she may poorly express this. The relationship between Bubby and Flapjack proves that you do not have to be related to be family. K'Nuckles is another story. He's a drunkard, a liar, a theif, a bum, and a failure who often sweeps young Flapjack away in his highly-exaggerated (or completely made-up) tales of adventure, which blinds Flapjack from seeing his true character. Despite being a bit of a jerk and quite the anti-role model, he does express great love for Flapjack, even if he doesn't want to admit to it or if his methods of expressing his feelings for Flapjack are highly obscure. There are multiple references to his alcoholism through-out the series. I think his relationship with Flapjack proves that even less than perfect people can still be loving people. And of course, Flapjack is a painfully-naive wanna-be-adventurer. He's very dedicated and tries his best at everything he does. He's often swayed in the wrong direction by the ole captain, but isn't necessarily a bad kid.
There are a few minor characters peppered in--there's the bartender, Peppermint Larry and his (possibly fictional) manipulative, controlling wife, 'Candy Wife', and Doctor Barber, the surgery-obsessed local doctor/barber. Many characters are illiterate.
The show puts heavy-importance on creativity and adventure, which is always a good message for the children. The main trio have all shown dedication and hardwork and have promoted to "do the right thing" such as when a group of children make fun of Bubby and K'Nuckles, instead of going along with them for the popularity, Flapjack stands up for his friends, even after being called names.
Characters have gotten "high" and "drunk" are more than one occasion.
All in all, I think it's a good show with good messages and role-models, by they are often obscured by character flaws or reality itself.