The answer to this question can be found in Chapter Ten of this great novel. This narrates the second visit that Kit makes to Hannah Tupper's house. When she arrives, she finds Hannah buys spinning thread. However, when asked by Kit if she grows the flax herself, note how Hannah responds:
"Some of the families in town always bring me their flax to spin," she explained... "Fourpence a skein," she said. "Enough to pay the taxes and buy what I need."
Thus we discover that the flax is a form of employment for Hannah. It enables her to meet her living costs. We also find out that part of those living costs are actually taxes that she must pay because she refuses to go to church every Sunday. This clearly is another way that the book depicts religious prejudice and persecution. The fact that Hannah is fined for choosing not to go to church is shocking to our modern day minds, and yet this was standard practice for groups such as Quakers in those times.