Rationalism, as a "system of belief regulated by reason," might be expected to mean the opposite of irrationality, ignorance, and perverse prejudice. But in ordinary usage, general as well as theological, the use of the word is substantially different. It is generally employed as a term of reproach for those who, without utterly denying or attempting to overthrow the foundations of religion, make such concessions as tend to subvert the faith. They rely, more or less exclusively and blameworthily, on mere human reason instead of simply, frankly, and fully accepting the dicta of the divine word. An atheist would not be spoken of as a rationalist, nor would an irreligious, blaspheming freethinker.
Entry from Everybody's Cyclopedia,