Religious concerns were part of the Hakluyts' arguments. The younger Hakluyt was an Anglican clergyman, and like most contemporaries who sought to justify the expense and danger of colonization, he used religion. In particular, he sough to oppose English "reformed" Christianity to that of the Spanish, who he thought were trying to win souls among Native Americans in the New World. 

It is necessary for the salvation of those poor people who have sat so long in darkness and in the shadow of death that preachers should be sent unto them.

These people, Hakluyt argued, should be English, who would, he said, "distill into their purged minds the sweet and lively lines of the gospel..." The Indians would be rescued from "ignorance" and the influence of the Spaniards, who were tarred with the "black legend" which emphasized their cruelty to native peoples. The desire to win souls was certainly secondary to more worldly concerns, but like most of their contemporaries, the Hakluyts promoted colonization using a discourse that emphasized God's work as well as that of men. 

Source: http://nationalhumanitiescenter.org/pds/amerbegin/exploration/text5/hakluyt.pdf