It was basically a business decision. The Dutch West India Company had a large financial stake in the success of the colony, and ensuring that new settlers were treated with "moderation" was seen as necessary. The official response of The Dutch West India Company was the following letter signed by Abraham Wilmandone and David Von Baerle on April 16th, 1663:
We, finally, did see from your last letter, that you had exiled and
transported hither a certain Quaker named John Bowne, and although it
is our cordial desire that similar and other sectarians might not be
found there, yet as the contrary seems to be the case, we doubt very
much if rigorous proceedings against them out not to be discontinued
except you intend to check and destroy your population, which,
however, in the youth of your existence, ought rather to be encouraged
by all possible means. Wherefore it is our opinion that some
connivance would be useful that the consciences of men, at least,
ought ever to remain free and unshackled. Let everyone be unmolested
as long as he is modest, as long as his conduct in a political sense
is unimpeachable, as long as he does not disturb others or oppose the
government. This maxim of moderation has always been the guide of the
magistrates of this city, and the consequence has been that from every
land people have flocked to this asylum. Tread thus in their steps,
and we doubt not you will be blessed.1
1 Shotwell,Ambrose Milton. Annals of Our Colonial Ancestors and Their Descendants, Or, Our Quaker Forefathers and Their Posterity, p 207