The government of England in the age of Elizabeth I was very different to what it is today. Queen Elizabeth was very much a ruler, unlike the monarchs today who are largely figureheads, and had to make all the major decisions of government herself. But Elizabeth could not do everything herself, and so she had various councillors and officials to help her govern the country justly and wisely.
The Queen was not above the law, but had to act in accordance with it, but Elizabeth was still a very powerful woman. No law could be passed without her consent. She could decide the religion of the country, decide when parliament was going to sit and what they could discuss, decide when and if the country was going to go to war, make decisions about education, the welfare of her people, even what food her people could eat and the clothes they were to wear. She also was responsible for choosing the men to help her govern, and had the power to send men or women to prison and order executions. Everyone in the country had to obey her. Not to obey her was against the law, and could be treason, for which the penalty was death.
The most powerful men in the land were those that Elizabeth chose to have around her. These were largely courtiers. Powerful men did not have to hold positions of power in the land. For some years Robert Dudley did not hold an important office, but was very powerful because of his close relationship with Elizabeth.
Elizabeth governed the country with the help of two very important institutions. The Privy Council, and it's daughter bodies the Council of the Marches and the Council of the North, and Parliament.