Why did some people find the ideas of the enlightenment disturbing?

During the Age of Enlightenment, people continued the questioning of traditional authority that had begun in the Renaissance, causing changes to ripple throughout society. By questioning the traditional explanations for the world, for example, scientists began to investigate the world as it really was, carrying out experiments and making observations of the natural world. Edmund Halley, for instance, identified the orbital pattern of the comet that bears his name, and Antoine Lavoisier discovered and identified oxygen and hydrogen and identified the role that the former plays in combustion.Questioning authority also had huge effects in the political realm. Philosophers such as John Locke, Jeremy Bentham, Thomas Jefferson, Montesquieu and Jean-Jacques Rousseau began to question the traditional organization of power in which noble elites ruled, sometimes capriciously, over a group of relatively powerless common people. Instead, they called for a more democratic society in which the government existed to protect each person's natural rights and had a balance of power that did not permit any one person or group to rule by fiat. These political ideas led to the revolutions in France and America and ultimately influenced governments across the world. 

Thinkers in the Age of Enlightenment stressed the ideas that traditional authority was not always correct, and humans could and should improve themselves through reason. This period saw numerous advances in science and massive political changes in Europe and North America

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