Tom knew Michael better than anyone. He had to have known that, once Michael found out about Fredo's betrayal, Fredo was a dead man. I think Tom had a certain empathy for Fredo--fellow "losers" according to how Michael felt about them. But, Tom would never have dared to warn Fredo about his impending doom for fear of his own life. And, I think the consigliere in Tom would have accepted that Fredo had to die because his betrayal--for personal gain--nearly cost Michael and Kay their lives.