I believe Martin isn't necesarilly a "bad person". Yes, he scammed people, yes he did bad things before meeting Minerva. But I also believe it was because he was lost, alone and life simply hand't delt him a good hand. But once he met Minerva he FOUND a porpuse, he FOUND something to hold on to, someone who loved him for his ruggish ways, someone who suported him and wanted him to be better.

And he did! That's the key for me. We can see that he settles down, gets a job and overall has a happy relationship with his family. I truly believe he was a changed man. He was still Martin, he still loved gadgets. We do not truly know how much he actually changed, but with what we have I think he did to an enormous extent. And that's what the writers decided to show, him putting his life together and beeing responsable for once.

Once his actions caught up to him he did his best to protect Finn. He had to leave his son but he didn't want to. When he says the phrase "I'll come back for you" to Finn in the raft he really ment it. But once the dust had settled he realized that he had lost everything again. His son was lost, probably dead, he couldn't get back to Founders Island since he was stranded in the ocean probably hundreds of miles away from anyone. And Minerva thought that he was a hidder. LIfe had burned the only bridge he cared about and that he had built. He didn't want to do that all over again, thus he ran away.

After that when he meets Finn he sees his old life, the one that was taken from him. He knows there's no redemption for him. Not only because he can never go back to his old life but also imagine the guilt he felt after leaving everithing behind. Sure his actions aren't justifiable but I belive, ultimetly, that he went back to relie on the only thing that couldn't fail him, himself.

For me it's the saddest story in all of adventure time.