What is often the first step to religion becoming harmful, and certainly the step that most skeptics should be concerned with, is when a person confuses religious belief with proven fact. It becomes dangerous when believers say that their beliefs are logically proven through agreement with a specific religious leader, or his interpretation of a particular text. Those who are most critical of religion often state that humanity would benefit if all religion vanished, for surely then there would be no more blind faith, and dispassionate, level-headed reason would take control of human thought. However, this is probably not the case since irrationality has many motivations. Humans are capable of taking advantage of one another in the same way that medieval bishops did so long ago, even in the name of science itself.
Medical quacks take great pains to cloak their claims in scientific jargon.
Modern charges of racism and sexual harassment are closer to medieval heresy trials than today's politically-correct spin doctors would have us believe. The core of religion is faith, which is belief without knowledge. Religious faith typically deals with spirituality, morality, and the great unknowable ultimate questions of existence. As such, religion deals with entirely different subject matter, goals, and rules than science. Science and skepticism are about the knowable, about building an ever more accurate model of the physical universe.