It's amazing how we all have different ideas, thoughts and takes on many scenes and lines in the trilogy. That's what makes this trilogy one of the best in history!

I've always taken what Michael says to Tom in that scene as a reminder to Tom that at one time, a young man named Michael, who had absolutey no involvement with the family business, came up with this idea to kill a Police Captain and a mob backed Drug Lord. And those who were involved in the family businss laughed at him, basically telling him that it was impossible to kill a police captain and get away with it. Then after some convincing those same 'experienced mob experts' realized that the kid actually had a good idea, and agreed to put the plan in motion, and the family was saved.

In other words, without coming right out and saying it, Michael's "If anything in this life is certain - if history has taught us anything - it's that you can kill anybody." to Tom was his way of saying to Tom, "Remember what we once pulled off to save this family?"

That's what I always thought that Michael was reminding Tom of.