Jesus often asked questions of His questioners, to help them think it through logically and see whether their question is even valid. So follow His example. People who pose this question seem to be saying that whenever atrocities are committed by adherents of a certain belief system, then that belief system cannot be true. Let’s see how that applies to the belief of atheism. Atheistic governments have slaughtered millions of their people; for example, Mao Zedong was responsible for the deaths of approximately 75 million in China, while Stalin used famine and murder to kill another 10 to 60 million in the Soviet Union. So could we use that same reasoning to conclude that atheism cannot be true? How would your questioner answer that?
When it comes to religion, it is popular these days to defend the Islamic religion regardless of the actions of its most committed followers. Despite the countless atrocities that have been committed, and continue to be committed, in the name of Allah and based on commands in the Koran, many people make a distinction between the “radical” Muslims who commit these acts and the “peaceful” religion of Islam itself. Ask your questioner if he is ready to condemn Islam and all Muslims based on the actions of a minority. Most likely, he isn’t—he is interested in condemning only Christianity.
But He answered and said to them, “I also will ask you one thing, and answer Me: The baptism of John—was it from heaven or from men?” (Luke 20:3,4)