With 20/20 hindsight, and staying inside the film (fascinating as the Bugsy Siegal stories are) I think the key line comes just before the part about skimming, when Michael tells Moe that the casino isn't making money and "maybe we can do better." This is a veiled threat to Moe that Michael correctly believes that if Moe is moved out by force, his mentor and protector Hyman Roth will "let it go."

He then goes out of his way not to accuse Moe of skimming because that is beside the point, and it is not the fight he wants to pick.

Greene sees this and first counters with the comment "yo9u guineas are really something... I take fredo in when you're having a bad time...etc" to which Michael sets Moe straight that he took Fredo in because the Molinari family guaranteed his safety and the Corleones bankrolled his casino.

Green then ups the ante by telling Mike the Corleones don't have the muscle to move him out and that he "talks to Barzini" who will allow him to make a deal and still keep the hotel. Clearly this means Moe is in a precarious position because he is going to have to let somebody wet his beak if he is to keep anything.

This doesn't phase Michael who wrongly steps into the argument about Moe's slapping Fredo around. When he realizes Moe did it because Fredo was banging cocktail waitresses two at a time, he drops that argument quickly, and just says to Moe "think about a price."

Having already embarrassed Michael, Fredo then makes things worse by going to Tom and asking if Vito can intervene for Moe...thus the harshness of Michael's warning to Fredo to never take sides against the family again.