Benvenuto, Flora!
1. Though Michael says to Fredo, "Roth wants me out," Michael is the one who wants Roth out. Roth and Vito Corleone had been partners, but only in the Prohibition-era booze business. But Michael had been greedily horning in on Roth's Western gambling empire even before Vito died. The first business deal we saw Michael involved in when he returned from Sicily was to push Moe Green, Roth's best friend, out of his Las Vegas hotel; later he had Moe killed because he resisted. By late 1958, when we first meet Hyman Roth, Michael has moved his entire operation to Lake Tahoe, owns three hotels in Nevada, and is about to force Meyer Klingman out of a fourth hotel, owned by Roth and the Lakeville Road Boys. And it's obvious that Michael has designs on Roth's Havana gaming empire. Small wonder Roth feels threatened! Roth has been buying time by pretending he's a kindly elder statesman, in the twilight of his years, who regards Michael as his surrogate son and heir. But he's plotting all along to kill Michael—there isn’t room for both of them.
2. When Michael visited Roth in Florida, he told Roth he blamed Pentangeli for the attack on his home and said he would kill Pentangeli. Instead, he sent Pentangeli to make peace with the Rosato brothers. Roth knew that Michael would never give an enemy a pass. So he assumed that Michael really didn't suspect Pentangeli in the attack on his home--meaning that he might suspect Roth. So Roth ordered the Rosatos to kill Pentangeli to eliminate Michael's main ally in New York.
3. Just before Michael left Tahoe, he told Tom: "Right now, you're the only one I can completely trust." We must take this to mean that he suspected everyone--including Fredo. You were right when you said he looked at Fredo suspiciously several times in Havana. But I don't think Fredo was his top suspect. I believe he was genuinely devastated when Fredo made his fatal slip-up at the Superman show.