This is a very interesting question, as these are not two characters one would normally put together. However, one way to find a connection between them would be through a focus on the two characters' religious experiences. Both Maggie and Faustus are centrally concerned with the Christian religion and with moral choices.
Maggie Tulliver has a painful childhood, but one informed by religion. For example, as she pounds nails into her doll's head to relieve her own sense of pain, she envisions herself as the Biblical Jael driving a tent peg into the head of the enemy Sisera to help save the Israelites. Her directing of violence against a doll (a proxy for herself), however, subverts the religious message of the Biblical story, much as Faustus's rejection of God's word (his Satan-prompted belief that damnation is inevitable) subverts the Biblical story.
As an adolescent, Maggie becomes more religiously conventional and turns her attention and devotion to reading Thomas à Kempis. Through his works, she embarks on a path of self-denial that is a sharp contrast to the path of empty self-indulgence on which Faustus embarks after he sells his soul to the devil.
Both Maggie and Faustus are caught between temptations: Maggie has to decide between her passion for Stephen Guest and her family, and Faustus between the devil and humbling himself to ask God for grace and forgiveness. Maggie chooses the path of renunciation; Faustus, in contrast, can't get over his pride for long enough to realize that God truly will forgive him. He thus heads down the path of damnation. Both characters in the end die, and both leave us with questions about the choices they have made—which, of course, encourages us to think about these choices.