Tom knew that Fredo was involved in the Tahoe shooting. When Michael returned from Havana and was alone with Tom, the first thing he asked was, "Where's my brother?" And Tom knew he was in NY, so he had to know why he wasn't back in Nevada with Michael. Also, at Mama's wake, Fredo asks where Michael is, and Tom says Michael "is waiting for you to leave." After Michael learns that Pentangeli is alive, Tom tells Michael that "Fredo says he knows nothing--and I believe him," even though, as we saw later, Fredo knew plenty. I think Tom had a soft spot for Fredo.