Right: the government of England had a problem with religious sects and needed to push them out somewhere. That created demand on the part of Puritans who didn't want to get hanged at home, to emigrate, and King happily approved it because it meant good riddance.
Well, with those territories not having defensible or Christian state, from standpoint of XVII century, those were exactly the same: those lands were "empty" and those settlers, by settling there as royal subjects, claimed it for the Crown.
If they settled in some country rules of which they'd find obliged to obey - either because it was Christian, or because it was too strong to ignore with their forces - they couldn't claim land and instead, will become immigrants, then of course it's not colonisation.
The lands were claimed for the Crown years earlier in the first grant to the Virginia Company, which gave them lands ranging 100 miles inland from the coast and from the 34th to 45th parallels. (http://www.let.rug.nl/usa/documents/1600-1650/the-first-virg...) It's why they made the Popham Colony. The first wave of Puritans to migrate weren't even living in England at the time, they had already moved to the Netherlands.
