I agree with Turnbull that Michael had been suspicious of Fredo even before the New Years party which confirmed Fredo's guilt. I think Michael may have begun suspecting Fredo all the way back to the night of the Tahoe shooting. If you notice, the one person who is not shown in any of the footage immediately after the shooting was Fredo. We see Deeana, Rocco, & Tom, and various buttonmen. Now that I think about it, Neri wasn't seen by the viewer either. However, the viewer never saw any action by Neri that would make you believe that he would betray Michael. As a previous post said, Fredo took sides with Moe Green back in the first film. Look at another traitor - Tessio. Sal openly questioned Michael's tactics at the meeting announcing Michael would be taking over the Corleone Family.

If nothing else, the long train ride gave Michael time to think about who the traitor was. He probably had a very short list of suspects by the time of the first meeting with Roth.