The previous answer gives you a number of possible definitions of a charter, but does not tell you which one applies in this book. In this book, the charter that the colonists have is like a constitution. This goes along with the first definition of charter as a noun in the answer above.
English colonies in the new world were typically given charters. These documents spelled out the rules for how the colonies would be governed. They specified what rights the colonists would have. In this book, the English government is trying to change the terms of the charter to reduce the degree to which the colonists' rights will be respected.
used as a noun
1. a written grant by a country's legislative or sovereign power, by which an institution such as a company, college, or city is created and its right and privileges defined
2. a written constitution or description of an organization's functions
3. the reservation of an aircraft, boat, or bus for private use
4. an aircraft, boat, or bus that is reserved for private use
5. a trip made by an aircraft, boat, or bus under charter
used as a verb
1. grant a charter to (a city, college, or other institution)
2. reserve (an aircraft, boat, or bus) for private use