Rosicrucians in those times worked secretly in behalf of freedom of thought, inquiry and investigation of scientific truths, and for the freedom of thought and worship for all people. 

The ideas and objectives of scientific research and study were scrutinized by authorities of the Holy Roman Church.   As scientific discoveries were found, they were subject to being labeled as heretical, because they contradicted the dogma or rule established by religious authority. 

René Descartes [1596-1650], John Milton [1608-1674], Benedict Spinoza [1632-1677],  and countless others wrote volumes of literature in disguised language, concerning the demonstrable, immutable and universally applicable spiritual laws that continuously operate within given conditions, even with the rule of erroneous Church doctrine.

Such thinking as the Copernicus concept of the Sun instead of the Earth being the center of the Universe; or of God as being pantheistic or in all of Nature and the universe, rather than the idea of being an anthropomorphic white-haired man on a cloud, contradicted the doctrinal rule of the Church, and was a political threat to the ongoing stability and power of religious authorities.  As was Galileo [1564-1642], who was condemned for heresy in designing the telescope and demonstrating the reality of the theory of Nicolaus Copernicus [1473-1543] —thousands were condemned by the Church Inquisition, that was first established in the 13th Century and in force through the 16th Century Reformation. 

Even though monarchs held the reins of power in their kingdoms in what today is known as Europe, for centuries even kings and queens had not defied the rule of "Rome" in establishing certain laws for individuals in their kingdoms, from fear of their own loss of salvation in heaven.