Batman is a man who believes in the law, but what happens when the law itself goes to far? Amanda Waller is a powerful force with the US Government, and believes that sometimes you need to conscript bad people to do good things. Thus, she made the Suicide Squad, something Batman has clashed with many times over.
Batman doesn't approve of using killers and psychopaths to do "good" things. And yet, Waller doesn't care, cause she believes she's right. She doesn't fear Batman, and has held her ground against him many times over.