Michael the Manipulator played Tom like a violin. The fact is, he needed Tom (for once) because (for once) he told the truth: "Right now, you're the only one I can completely trust." The reason he didn't tell Tom that he already knew Roth was behind the attack was that he'd kept Tom out of all the previous Roth negotiations--and even at that dire point, he wasn't going to let him in. If Tom had known that Michael blamed Roth, why, he'd actually be capable of making some decisions on his own--like (as dt said) looking closer into Pentangeli's alleged "death." Heaven forbit, he might even have been more useful to Michael--a real consigliere.