The quota system was unfair to these immigrants because it did not allow them to come into the US in large numbers.
In the 1920s, people from these areas were seen as negative influences on the US. They were said to be less likely to assimilate and more likely to cause problems than previous waves of immigrants from Northern and Western Europe. Therefore, laws were passed that set quotas based on the number of people from a given country who had been in the US in 1890. That year was chosen because it was before many people had started to come from Eastern and Southern Europe.
The quotas, then, were unfair because they allowed fewer people to come from these regions than from other parts of Europe.
The quota system that was instituted by the Emergency Quota Act of 1921 was largely unfair to Southern and Eastern Europe because it was based on percentages of immigrants coming from countries based on the 1910 census--before revolution and war made many Eastern Europeans refugees. The Emergency Quota Act kept up quotas from Western and Northern Europe but did not allow for increased numbers of Southern and Eastern Europeans, because there was a push in this country during the 1920s to keep out Communists and anarchists. There was fear that this country would suffer a communist revolution similar to what happened in Russia and while the Soviet Union did attempt to start revolutions worldwide, many people who wanted to immigrate to America only wanted better lives for their families. This act also played into America's xenophobia against Catholics and Jews of the period, as the Ku Klux Klan enjoyed a resurgence during this time in history.