Nativity Scenes aren't what they seem...
Every Nativity Scene depicts a Holy Family, complete with Mary and Joseph looking down at their new Baby. It is easy to forget, when looking at such a holy scene, that this is not a typical nuclear family with a biological mom and a dad. Joseph is not Jesus' biological father, since it was the Spirit that helped Mary to conceive (Matthew 1:18). Mary is Jesus' biological parent, while Joseph is His Step-Father.
To be clear, this in no way lessens the sanctity of that family, nor is it intended to diminish Joseph's role as Jesus' earthly father (nor is it meant to diminish the vital role of any adoptive parent or step-parent!). To the contrary, it could be said that this non-nuclear detail about the Holy Family actually enhances their sanctity because this makes them more incarnate in this earthly world.
It is a source of comfort that Jesus Christ, Redeemer of the World, comes from a non-nuclear family because from the very beginning, He breaks the "mythical norm"* which seeks to exclude and marginalize God's people. Jesus not only brings about God's love for all of God's people, but He also represents the perfect imperfections of humanity, making His love all the more accessible and present.
Mary's Family Tree is Intentionally Flawed
The Gospel of Matthew includes a genealogy of Mary, the mother of Jesus (notice, it is not a genealogy of Joseph!). The stories attached to the names mentioned in Matthew's genealogy span from incest, infidelity, rape, prostitution and polygomy.
See also: Sex(ism); Jesus' Family Tree