The burglars then went over their files, and found what seem to me to be pretty silly things, like FBI agents being instructed to create the perception that the organizations they were investigating had many FBI informers and agents in them.
They passed on the files to a reporter anonymously. Reporters and later investigations by Congress revealed more details about the FBI's cointelpro project, wherein the FBI committed illegal sabotage against groups they were investigating.
Who are the good and bad people? Well, the FBI is bad for committing illegal sabotage. The burglars are good for getting important information, but bad for doing it by stealing random boxes of files - which might've hindered legitimate investigations. The reporter is good for publishing her story. Congress is good for investigating further but bad for doing nothing effective to curtail abuses by American federal intelligence agencies.