In short, because although it was heavily suppressed, the Orthodox Church in Russia was never completely extinguished. The resurgence of the Russian Orthodox Church after the fall of the Soviet Union is, in my opinion, an excellent case study in the endurance of culturally ingrained institutions even in the face of government sponsored attempts to stamp them out.
To start, let’s briefly review the history of the Orthodox Church in Russia. Christian missionaries Cyril and Methodius were responsible for some of the first major mission attempts among the Slavic peoples North of Greece. They devised a written script for Slavic languages, which eventually developed into the somewhat anachronistically named Cyrillic alphabet still in use in Russia today. The Russian prince Vladimir became the first major Russian ruler to be baptized in 988, when “Russia” was but a loose collection of competing principalities. As these principalities coalesced into the Russian Empire in the second millennium, Orthodox Christianity developed alongside it. The identity of the two were intrinsically connected. On the eve of the Russian Revolution, Orthodoxy was part and parcel of the Russian identity. In the 19th century there had even been a resurgence of interest in the Orthodox spirituality in part as a result of the slavophile and “pochvennichestvo” movements epitomized in the literature of writers like Nikolai Gogol and Fyodor Dostoevsky. Even as Bolshevik fever swept the nation, any attempt to stamp out Russian Orthodox faced an uphill battle.
The two revolutions of 1917 and subsequent civil war in Russia afflicted the Orthodox Church with confusion and disaster. Many Orthodox clergy and monastics were killed in the October Revolution, a trend that continued under Lenin’s policy of seizing church property. Perhaps most famous among these “new martyrs” was the Tsarina’s sister Elizabeth, who had taken vows as a nun following the death of her husband, Grand Duke Sergei. Yet it was precisely such confusion and uncertainty that allowed the Orthodox Church in Russia to attempt to carve out an existence in the face of political adversity. St. Tikhon of Moscow, the bishop of Yaroslavl and former Archbishop of North America, was quickly elected as Metropolitan of Moscow and, once the decision was made to restore the Patriarchate, then elected to the position of Patriarch of the Russian Orthodox Church even as the Bolsheviks secured their control of Moscow. Patriarch Tikhon was deposed by the Soviet Government in 1923 but this was never recognized by the Orthodox Church. He died in 1925.
During the Russian Civil War, many fled or were exiled from Russia. Russian migrants flocked to the newly established Kingdom of Yugoslavia, as well as already established expat communities in cities including Paris, Shanghai, and San Francisco. These communities became a major factor in the survival of Russian Orthodoxy. The Russian Orthodox Church Abroad (ROCA) firmly established themselves as successors to the Russian Church who were independent of the USSR’s influence, and enjoyed the support of other major Orthodox Churches. Paris became an important epicenter of Russian Orthodox thought, serving as the home to famous exiled theologians Sergei Bulgakov and Vladimir Lossky, as well as spiritual leaders like St. Maria Skobtsova. In Shangahi, Archbishop St. John Maximovitch led a small but important community of Russian exiles and expats, who would later flee to the Phillipines in the face of the communist revolution in China, and eventually settle in San Francisco. The early years of Stalin’s regime were a desperate time for the Church. Upon his death, Patriarch Tikhon foresaw that the church would be unable to hold an election for the next patriarch and so started a game of ecclesiastical hot potato by naming three successors, who in turn also named successors as arrests and executions swept the nation. The potato finally landed in the hands of Metropolitan Sergius, who assumed the role of “acting Patriarch” in 1927. Controversially, Sergius declared that the Soviet Government had the support of the Russian Orthodox Church. This decision led to a break in communion with ROCA and other Orthodox bodies outside Russia, but crucially secured nominal toleration by Stalin’s government. Yet Stalin’s anti-religious programs continued and by 1939 only a couple hundred churches in Russia remained open, with a severe lack of clergy to service them.
Soviet policy toward the church was dramatically reversed upon Germany’s invasion in 1941. Patriarch Sergius threw the full support of the church behind the Soviet war effort. In doing so, he secured major concessions from Stalin’s government, which was desperate for any and all support. From the Oxford Dictionary of the Christian Church (cited below): “The resulting concessions by the Soviet government allowed the reopening of some 20,000 Orthodox churches, eight seminaries for the training of clergy, two academies for advanced study, and some monasteries…” Crucially, Sergius died in 1944 and the government allowed for the election of a new Patriarch, Metropolitan Alexis of Leningrad, in 1945 just before the hammer and sickle once again began to swing down in a campaign of religious suppression.
After 1945, the Russian Church experience similar waxing and waning of eras of persecution. The official state atheism of the USSR was tempered by the political advantages a cooperative church provided. For example, the religious loyalties within Ukraine had long been divided between Orthodox and Eastern Catholic factions. Toleration and cooperation with the Orthodox Church allowed the USSR to apply religious leverage against Easter Rite Catholics in Ukraine, the existence of whom opened the door to troublesome meddling by the Vatican. Similarly, missionary efforts by Western evangelical groups could be suppressed in the name of Orthodoxy, closing the door to Western interference and espionage via missionary activity. The Patriachate endured throughout the Soviet era, with the election of Pimen I in 1970/71, and Alexy II in 1990.
In summary, there were a couple of key factors that contributed to the Russian Orthodox Church’s survival during the Soviet era. The civil war between 1917 and 1923 gave the Russian Church crucial time to prepare by establishing a hierarchy after the abdication of the Tsar, and by allowing exiles to flee abroad. Although relatively small, the Russian Orthodox Church abroad provided fertile soil for Russian Orthodox identity and spirituality to continue to flourish. Within Russia, even Stalin was aware that an institution as old and culturally important as the Orthodox Church in Russia could not simply be stamped out. The best that even the most radical Soviet policy makers could hope for was to extinguish the church over a series of decades. On a pragmatic level, there were also benefits to allow the church to continue to operate, albeit in a heavily restricted way.
By time the USSR collapsed, the leadership of the Russian Orthodox Church was left standing, and soon bolstered by the return of exiled Russians and resumed communion and cooperation with the other Orthodox churches. In addition, subsequent post-soviet governments have played an active role in returning historic church property, and building new churches over the site of historical ones that had been destroyed. But most importantly, the Orthodox Church was able to “return” to the nations of the Eastern Bloc simply because it never left.
Citations and References
Most historical data for this answer was sourced from:
"Russia, the Soviet Union, and the Commonwealth of Independent States, Christianity in." In The Oxford Dictionary of the Christian Church, edited by Cross, F. L., and E. A. Livingstone. : Oxford University Press, 2005.
For those interested in the the lives of prominent Russian Orthodox figures in the 20th century, I recommend:
Pearl of Great Price: The Life of Mother Maria Skobtsova, 1891-1945 by Sergei Hackel
Exodus: St John Maximovitch Leads His Flock out of Shanghai by John B. Dunlop
It should be noted that these books are written by Orthodox Christians and reflect their beliefs as to the truth of the Orthodox faith. That said, this does not diminish the value of the historical information they provide.
EDIT: After being featured in the Sunday Digest I've returned to correct some typos.