While the 1990s brought an era of cultural libertarianism and market economics, the sudden onslaught of Capitalism, its values and effects, led to a degree of social reaction.
One unforeseen aspect of the collapse of the USSR for Central Asia was a revival of Islam, and this was in no small part affected by the jihadist fervour just to the south of the Soviet border. Though the Afghan War ended for the United States in 1989, it did not end for Central Asia. The United States had funded numerous groups, some of which agitated even within the borders of the USSR, something largely forgotten today. The spread of Salafi, Deobandi and Wahhabi forms of Islam greatly affected the region and there was something of a revivalist spirit in the air.
The 1990s also brought a new wave of Christianity and contacts with the West and as Capitalism began to disappoint and indeed the Central Asian '-stans' had little or no context for it, a degree of bitterness set in. This found outlet in not only anti-Soviet but anti-Western narratives and ethical imperatives. Christianity so unfortunately associated with Western Capitalism would also suffer as a result.
While many of the ex-Soviet bureaucrats were happy to do business with the West, they were forced out of pragmatic concern to embrace mild and secular forms of state-sponsored Islam. As the radical movements grew in power and influence they targeted morally compromised secular regimes. To maintain legitimacy the governments of Central Asia embraced Islam and trying to wrest away the narrative from the radical fighters. The state became zealous for Islam only to counter the more fanatical claims of the terrorist-fighters.
One is reminded of Conrad Adenauer's government in West Germany. Though he himself had no ties to the Third Reich, his government (and military) was actually filled with numerous ex-Nazis. He didn't like them but for the sake of expediency (and often at US behest) he accommodated them. And though few today realise it, there was substantial support for them in the German public. This continued for several decades after the war. The fear of Communism kept the German Right alive.
The embrace of Islam by governments in Central Asia was in many cases probably less than genuine, for these same figures were in most cases, ex-communist party members who were simply trying to maintain power.
Sadly, the Christians of the region have been caught in the middle. The state in embracing a pragmatic Islam is unfavourable to them and doesn't want to show favour to them in any way shape or form. And of course the radicals want to eliminate them or at the very least drive them away.
US calls for human rights only add fuel to the fire, embittering the state bureaucracy and further identify religious minorities with Western imperialism and thus decadence.