The thing about adventure stories is that a lot of the characters are really just there to serve as mechanisms to move the plot forward. Stevenson's main characters have more meat on them, but he still needs to keep the plot going. Ebenezer is a good example of a simple, plot-moving character. He is the (evil) engine who sends Davie on his adventures by arranging for his kidnapping.
In the end, Ebenezer's backstory isn't that exciting: he got into a fight with his older brother, Alexander, over a woman (Davie's mother). The woman chose Alexander, and Alexander made a deal with Ebenezer that he could have the Shaws estate if Alexander got the woman. Because he's greedy and wants to protect his property, Ebenezer tries to kill Davie by tricking him into walking off an unfinished staircase. Then he attempts to sell him into slavery via Captain Hoseason. In the end, Ebenezer is really just a weak, selfish man.