The Protestant Reformation was mainly against the Roman Catholic Church of Europe, this movement was against some practices that happened during that time. Protestantism argued that the Roman Catholic Church was getting away from the bible and because of that the movement insisted on the importance of the scripture and the importance of personal faith in salvation. This led to a freedom of religion and emphasis on personal faith and conscience, that was also important in the advance of individualism - Enlightenment - and the liberal reforms that came later with it.
The Scientific Revolution was also important because it removed scholasticism and the beginning of modern science. The creation of methods of observation, experiments and reason. These new methods brought scientific advances that expanded science. All of this also resulted in the application of the scientific method to humanistic, social and political issues that pushed the advance of individualism.