I just read an excellent book about this! It is called International Politics of Central Asia by John Anderson. I can't recommend it enough! Now, before I get to how Muslims were treated, I need to explain what Central Asia looked like at the time and how it became that way.

      Basically, in the 1800s, Russia was expanding its borders into Siberia. As it was doing this, it wanted to trade with the local leaders across the Steppes. The nomadic horsemen that resided in the Steppes, however, had other plans. Oftentimes, they would harass Russian traders, either killing/robbing them or charging them a hefty 'protection fee'. As can be expected, this angered Russia. They sent troops into what they dubbed Turkestan (all of Central Asia) and began to make deals with Tartars and other powerful groups to protect Russian interests. They slowly began to play groups off of each other and annex more and more land.

Eventually, Russia and Britain were competing for control of Central Asia. This is called the Great Game. Britain wanted to protect India, while Russia wanted to protect its new, extremely underdeveloped territories. They reached a stalemate in influencing Afghanistan, which is where the Great Game ended.

Russians began to slowly trickle in to these new territories, particularly Kazakhstan and Uzbekistan. The former had ample coal, oil and natural gas connected to Siberia. The latter, on the other hand, had a HUGE supply of cotton (more on these topics later). While there were on again off again attempts to promote Russian as the official language, Russia had more important things to focus on, like the rising Austro-Hungarian Empire and Japanese Empire. The region was largely ignored until after WWI and the Bolshevik Revolution^1 .

During the reign of Stalin, there was a renewed focus on the newly minted Central Asian SSRs. The borders of what we know today as Kazakhstan, Uzbekistan, Turkmenistan, Tajikistan and Kyrgzistan were drawn up to promote ethnic and regional tensions, which lessened the chance of all out rebellion against the USSR. Stalin began to emphasize state atheism, which meant that all of those pesky mosques had to go! The governors of the SSRs, however, only shut down a small amount so as not to inflame tensions^2 . There were also major attempts made to make Russian to official language, however the people seldom adopted it. Anderson notes that most of the Soviet governors couldn't even understand the regional languages! The Soviets began a campaign of 'Russification', where they changed towns and roads to Russian names.

After Stalin's death in 1953, Krushchev took over. He ended the Russification of Central Asia during his de-Stalinization campaign, however he heavily encouraged Russian immigration to the region. While religious restrictions were not as harsh, the region was still extremely exploited. Cotton, which made up 70% of Uzbekistan's economy, was shipped to other parts of the USSR. However, Moscow was demanding more cotton then the already overworked people could produce, which lead to them overreporting the cotton yield. In this same time period, Central Asians had an interesting time dealing with passports. Many ethnic groups, particularly the Uzbeks, were spread about all the -stand. The USSR demanded that they pick one ethnic group to identify as. Is you mom Turkmen and your dad Kazakh? You might as well flip a coin to decide what you want on your passport. Anderson states that this was to inflate ethnic differences.

^1 There were several revolts against the Soviets after the Revolution, however they were crushed in short order.

^2 Despite this, the Central Asian region today doesn't have as strong a relation to Islam as other nations like Iran and Afghanistan do.