Two reasons: either the Bolsheviks crushed them, or their conditions improved enough that they had no reason to go on fighting.

The "Green armies" is an ambiguous term, it merely refers to the armed paramilitaries unaffiliated with the war's larger factions: the Reds, the Whites, the Blacks, etc. There was no united "Green Army," just many bands around the country, usually formed of locals pissed off with the tribulations of the war and prepared to defend their communities.

The biggest reason for countryside resistance was the Bolshevik government's requisitioning policy. The Reds initiated a policy called "War Communism" which Lenin likened to a "crusade" for bread: A "merciless and terroristic struggle and war against peasants and other bourgeois concealing grain supplies." Bolshevik soldiers went to villages and confiscated food supplies, and they used brutal means if they encountered resistance. Villagers were beaten, or heavy fines were imposed on people found to be hiding food. By January 1919 the Bolsheviks were requisitioning fruits, vegetables, grain, animal feed, meat, eggs, and milk, and sometimes even animals. Obviously this had disastrous consequences for already impoverished communities.

Therefore many peasants either passively or actively opposed requisitioning through violent resistance. Sometimes this really did approach "army" levels: in 1920 more than 250,000 peasants in Tambov had formed the "Tambov Blue Army," and used hit-and-run tactics to put the hurt on the Reds. But ultimately these were poorly-armed peasants fighting against a real military, and in the end the Reds crushed the Blues as they did most other peasant resistance. The war in Tambov was especially cruel: the guerrillas crucified captured Communists to trees with railway spikes, ripped off their genitals, and branded their chests with a cross. The Reds responded with summary executions, aerial bombardment, and finally poison gas, eventually ending the rebellion. By 1922 most "Greens" had been crushed.

The outcome of the Civil War and the requisitioning was widespread famine. Although most of their enemies had been defeated, the Reds imposed martial law on areas like Ukraine where they feared renewed rebellion. But they also took proactive steps by introducing the New Economic Policy (NEP), which allowed a limited free market, and appealing for international humanitarian aid, which organizations like the American Relief Organization responded to. By June 1923 the situation had improved and lifted 10 million Russians from starvation. But at least 1.5 to 2 million had died of starvation between 1921 and 1922.

Source: Bruno Cabanes, The Great War and the Origins of Humanitarianism, 1918-1924