Maudie makes some attempt to explain this to Scout, who doesn't really understand the distinction either. Maudie starts to say that the reason Arthur Radley never left his house had something to do with his being a "foot-washing baptist," which confuses Scout, because she knows that Maudie is a Baptist, too. Maudie explains that she is "just" a Baptist—her "shell" isn't as hard as that of foot-washing Baptists. It's clear that Maudie is making a distinction between the two denominations; a foot-washing Baptist, or a primitive Baptist, is defined in Maudie's eyes as someone who believes all forms of pleasure are sinful.
Maudie gives the example of some passing primitive Baptists who told her that her flower garden was sinful and that it would send her to hell. They told Maudie that she ought to spend more time in the house reading her Bible, and less time in the garden. Maudie goes on to say that, in the minds of primitive Baptists, women are sinful "by definition," at which point Scout wonders if Arthur Radley stayed in his house to keep away from women (and other forms of potential sin).
In short, Maudie uses the term "foot-washing" in reference to the ritual foot-washing practiced by primitive Baptists, but really the distinction she's more interested in is the approach of primitive Baptists to sin and what is sinful.