During the Russian Civil War the majority of the Cossacks remained loyal to the White Army. Despite having several advantages over their enemies, they eventually fell to the Bolsheviks. Afterwards, they were dealt with through trial, exile, and execution.
The first opponents of Lenin’s regime to take up arms were the Cossacks in the south of Russia. While their will to fight the Bolsheviks was great, they had a fatal weakness, as Landauer explains: “Although the Cossacks were dangerous enemies because of their highly developed military qualities, in political matters their scope was utterly limited. They had no common goal except the defense of their property and they failed to understand that the success of this defense depended on the annihilation of the Soviet regime in all Russia, and not merely on local victories.” -(http://econfaculty.gmu.edu/bcaplan/museum/his1f.htm)