Cowardice is a lack of bravery. Boo Radley, Atticus, and Jem all show bravery at some points in the story. At other points, they seem to lack bravery, so one could say they display cowardice.
Boo Radley hides away in his house, never going out when people can see him. Although readers don't know his motivations for his reclusive lifestyle except through the insight provided by his history and town gossip--or the children's imaginations--when Boo rescues Jem and brings him home, he does seem to display some cowardice. He stands in the corner in Jem's bedroom and doesn't come near or speak to the others in the room. When Scout leads him back to the bedroom before she leads him home, Boo stands over Jem with "an expression of timid curiosity on his face." If one equates timidity with cowardice, then Boo exhibits cowardice here.
Atticus is portrayed as a highly courageous character. Throughout most of the book, he shows bravery rather than cowardice. However, if one strains to find an example of cowardice for Atticus, one might point to the time that he obeys his sister and talks to Jem and Scout about "how you must try to behave like the little lady and gentleman that you are." Atticus obviously doesn't want to give his children this talk about "gentle breeding," yet he seems afraid to defy his sister's wishes in this case. As he speaks to the children, his "collar seemed to worry him." Scout concludes that "Aunt Alexandra had put him up to this, somehow." So although Atticus stands up bravely before a mad dog, a murderous mob, and a foul Bob Ewell who spits in his face, he displays some cowardice before his sister.
Perhaps the strongest example of Jem showing cowardice is when he refuses to admit to Atticus that he was in the Radleys' garden. He sneaks back to get his pants even though he knows Mr. Radley is watching from his porch with a gun. He fears disappointing his father more than he fears being shot at. He tells Scout, "Atticus ain't ever whipped me since I can remember. I wanta keep it that way."
Cowardice is a strong term, and there may be better words to describe the reasons for Boo's, Atticus's, and Jem's behaviors. Each of them does display some lack of bravery, however, as depicted in these incidents.