Queen Elizabeth: Now, I ask you to pass this Act of Uniformity not Not for myself, but for my people, who are my only care.
Bishop: Madam, By this act, you force us to relinquish our allegiance to the Holy Father.
Queen Elizabeth: How can I force you, Your Grace? I am a woman. I have no desire to make windows into men's souls.
In historical context, Queen Elizabeth wanted to unite her people under a common prayer book. However she did not want to impose ways of interpreting it. Hence she uses the expression of not making "windows into men's souls" to describe her unwillingness to persecute people based on their interpretation of texts, as it is their soulful way of perceiving things. She does not see nor wants to control what goes on in the minds and souls of her subjects.