During this time, the soviets rose to power and pretty much became hostile toward the family and moved them from the Alexander Palace to Siberia and eventually a house in Ekaterineburg. The Soviets (The Red Army) were engaged in a civil war with parts of the country who did not want them to take over and as the other army (the White Army) started making progress near where the Tsar and his family were imprisoned. It was determined that they had to be killed so they would not become a rallying point for the White Army if they were captured. I think killing all of them and not just the former Tsar and the former Tsarvitch was simply eaiser for the Red Army instead of allowing the women and retainers to safely leave the country.
In addition to the Tsar and his immediate family, many other family members were murdered as well, including the Tsarina's sister who had become a nun.