Neither the Hakluyts nor John Winthrop were particularly interested in highlighting the challenges of settling the New World. Winthrop's Reasons to be Considered for Justifying the Undertakers of the Plantations in New England, in particular, is set up as a series of objections to the project followed by his answers to them. Essentially, he, like the Hakluyts, argues that there is no legitimate reason to object to colonization. For example, one possible objection that he lists is that "We have no warrant to enter upon that land, that has been so long possessed by others." He responds to this argument by saying that

That which lies common, and has never been replenished or subdued, is free to any that possess and improve it; for God hath given to the sons of men a double right to the earth — there is a natural right and a civil right. 

Because Wintrhop assumed that Native Americans had not "replenished or subdued" the lands that they lived on, from the standpoint of "civil right," they were there for the taking, as far as he was concerned. In response to the objection that the Jamestown settlement had experienced such great difficulty, Winthrop responded dismissively that:

1. their main end was carnal and not religious;
2. they used unfit instruments — a multitude of rude and misgoverned persons, the very scum of the land;
3. they did not establish a right form of government.

The Puritans' planned society would be different, he thought, and God would smile on their venture. 

For their part, the Hakluyts mostly emphasized the desirability of colonial expansion, touting its benefits in reducing the population of the poor (precisely the "very scum of the land" that Winthrop was referring to); its potential to spread Protestantism to allegedly benighted Indians, and the strategic advantages of checking Spanish aggression, which was viewed, thanks to the so-called "Black Legend" as evil and exploitative in any case.

http://www.winthropsociety.com/doc_reasons.php

http://en.wikipedia.org/wiki/Richard_Hakluyt