Throughout her reign, Elizabeth's main concern was the peace and stability of the realm, and religious persecution was only adopted when certain religious groups threatened this peace.  It was unfortunate for Elizabeth that so many of her contemporaries did not share her views on toleration, and she was forced by circumstance to adopt a harsher line towards Catholics than she intended or wanted.  Elizabeth's toleration of Catholics, and her refusal to make changes to the Church she established in 1559, has led some historians to doubt her commitment to her faith - even to assert that she was an atheist, but such statements are misleading. Elizabeth wanted a Church that would appeal to both Catholics and Protestants, and did not want to move the Church in a more Protestant direction, thus making it more difficult for Catholics to accept the Church than it was already. The form of worship also suited the Queen's conservative religion. She had little sympathy with Protestant extremists who wanted to strip the Church of it's finery, ban choral music, vestments and bell-ringing, and liked her Church just the way it was. 

Elizabethan hoped that by retaining the Church as it was, people would become accustomed to it. She wanted her Church to be popular with her people, and for Catholicism to die out naturally as people turned to the religion she had established. In this she was largely successful, for by 1603, the English nation as a population were generally Protestant, and Catholics were in the minority.  Elizabeth had her own private chapel in most of her palaces, and reputedly prayed there everyday. She saw herself as God's vessel on earth, and would pray to determine God's will so that he would reveal it to her, and she could implement it. Although Elizabeth's actual beliefs elude us, we are able to get an indication of them from her attitudes and gestures. Her chapels were conservative - the crucifix was displayed, and she also liked candles and music. She disliked long Protestant sermons, but also expressed displeasure at some Catholic rituals such as the elevation of the host, which implied that she rejected the Catholic belief of transubstantiation.  She also did not really approve of the clergy marrying as she expressed on several occasions, but as this was an integral aspect of Protestantism, she had to accept it. 

A more personal indication of her beliefs are the prayers she wrote for her people, and the letters she wrote to her friends and relations. In these letters she often referred to God and the need to accept his will.  In her prayers she also acknowledged her own faults and shortcomings. Elizabeth was by no means the perfect Protestant by the standards of many of her clergy - she swore terribly, using expressions that some thought were blasphemous, one of her favourite being "God's Death", and her sumptuous appearance was criticised by the more radical Protestants, known as "Puritans", who accused her of vanity and idolatry - but there is no reason to doubt that the Queen was a committed Protestant who took her faith seriously.