Bear in mind that Tom was Vito's choice for consigliere, not Michael's. He was "out" near the end of GF because, as Michael said, "you're not a wartime consigliere." He had failed to see the plot that resulted in Sonny's murder. "Besides," said Michael, "who's a better cosigliere than my father?" But when Vito died, Tom came back "in"--temporarily.
In Nevada, Tom was Michael's "legitimate" lawyer. He knew about the deal to buy into the Tropigala(sp?) because that was a semi-legit deal. But as you saw, he wasn't included in the Roth negotiations. The look you saw Michael and Tom exchange when Geary mentioned the Tropigala deal was probably a signal that they thought something was going wrong, that Geary would put the squeeze on them.
Michael meant it when he said that, right after the Tahoe shooting, Tom was "the only one I can trust." Michael gave him all that BS about keeping things from him because "you're my brother and I love you," and Tom practically collapsed with gratitude. Michael was playing him like a violin. As soon as Mike came back from Cuba, he was treating Tom like dirt.