Only Michael and Al knew.
Fredo thought he was forgiven by Michael as organized by Connie. Fredo ran from Michael before and he would have run again if he didn't really think he was forgiven. Tom would never have gone along with it had he known, but I think he had his suspicions when he saw Michael getting paranoid. Tom, after all, was very aware of how important family was to Vito as he was taken in and loved by Vito as a son. Tom was never sure of Michael until after the attempt on Michael's life, perhaps it was the age difference, but definitely Sonny didn't see Tom as a brother as shown by their fight after Vito's shooting. Tom even has to defend himself, "I was as much of a son to him..."
Vincent and Mary talk about Fredo's death when she asks Vincnet if she thinks her father had Fredo killed. Obviously there was at least a rumor of it and that rumor had to come from somewhere, likely Kay as she tells Michael, "Tony knows you killed Fredo." Connie would have suspected and then, later, realized the truth, resolving herself to Michael being strong for the family. Look at the shot, Connie and Michael are seated opposite each other as equals. Michael talks about his attempts to go straight and his regrets about the money and the killings and tells her about making his confession. Right after Connie says:
Michael, you know, sometimes I think of poor Fredo, drowned. It was God's will. It was a terrible accident. But it's finished.
That line would never have been said if she hadn't known given the context of the preceding conversation. Talia Shire's delivery says as much. She speaks with understanding and compassion, then tells Michael how much she loves him.
Fredo's death was one of those unique things that exist in families: open secrets. It killed Michael in the end. In becoming strong Michael became cold. Unlike Vito, he couldn't separate his family from his business and lost everything except the money in the end.
