In II, Michael kept Tom out of the loop unless and until he could not afford to keep Tom out of the loop. As others have stated, Michael made Tom the Don after the attempted murder simply because he could not trust anyone else. Also as others have stated, Michael uses Tom when Michael needs to use Tom and that that usefulness comes full cycle when Michael challenges Tom to go along with him or get out.
In II, Tom is still operating under the conditions which Vito and Michael had set up upon Michael becoming the Don.
That scene where Michael dismisses Tom ("he only manages parts of the family business") and Vito tries to explain why things are like they are (Vito is now playing the part of consigliere) is key. Perhaps there was a bit of "good cop bad cop" to it, but it strikes me that Michael's attitude towards Tom is cold and dismissive.
When Michael has to make Tom the Don, it certainly is an admission that Tom is the only person he can trust who has the skills and authority to act in his name. But it is true that by the end, when Michael out and out blackmails Tom by threatening to reveal his infidelity, that whatever Michael feels is Tom's value as a lawyer and a strategist, he has no real respect for him. Michael simply does not view Tom as a brother in the same way that Sonny did.
I also think, to some extent that by the end of II, Michael has so wholly been transformed not only by the attempted murder of himself and his family, but by Fredo and Kate's betrayal of him, that he really has become a completely solitary figure; isolated from humanity. That final scene of him looking out at the lake as Fredo is executed shows the man that Michael Corleone has become, so it's little wonder that he treats the only man left in his entire inner circle who he could conceivably trust completely with such disrespect and contempt. By the end of II, even Connie seems to have become little more than a functionary.
