Demonizing a group of "others" based on ignorance or prejudice is often used to maintain the power of certain political structures not through the force of their ideas, but through fear.
Characterizing intellectuals and scientists as ivory tower elitists or conspirators results in a society which doesn't value learning and mistrusts those who do. It leaves us unable to rationally address the challenges with which we are faced.
Different societal norms and cultural practices are not necessarily inferior just because they are different. Accepting this does not mean allowing injustice masked as tradition to go unchallenged
While atheists do not rely on magic or superstition as foundations for beliefs, it does not follow that everything we experience must be explained and understood. Sometimes its perfectly fine - perhaps even preferable - to not understand how something works or why it is.