Two reasons, I believe:
First, as Hevy said, Michael wanted Tom to be completely "legitimate" so he could successfully front for Michael in Nevada, where Michael intended to be "legitimate."
Second, Michael told Tom, "You're not a wartime consigliere." I believe he meant that Tom lacked "Sicilian cunning" and "ruthlessness"--qualities that Michael may have felt could have prevented the Five Families War of 1946, Sonny's death and Michael's own succession to the Donship. In the novel, Tom blames himself for Sonny's death. "He was, he knew now, no fit consigliere for a family at war. He had been fooled, faked out, by theFive Families...Old Genco Abbandando would never have fallen for it, he would have smelled a rat...tripling his precautions."