The best evidence we have of Daniel Hutt's family is actually in the profile of his brother John Hutt. Both a proceedings in London in 1671 as well as Daniel Hutt's will show that Daniel had a brother John in London who was said to be age 31 in 1671.
There is a John Hutt baptised 1640 in London as the son of William Hutt, cheesemonger, and his wife Hana; this is the right timeperiod to be Daniel's brother John. The author of the original GEDCOM therefore concluded that both Daniel and John must be sons of this couple.
So far as I can tell no evidence has been produced from a will of William Hutt, nor is there a baptismal entry showing William Hutt as the father of a Daniel; thus, this seems very slim evidence.
Of course, geni.com and FindAGrave have no evidence at all.
I would conclude that we have no real evidence of his parentage. Note that the Early Colonial Settlers of VA and MD website, which tends to be conservative, shows him without known parents.