"Sometimes there's a mother," the narrator intones. "Sometimes there's a father. Sometimes there's a father and a father. Sometimes both fathers are mothers." Eventually, the little boy is spirited down a sewer by a friendly crew of crated monsters.
"Families come in all shapes and sizes," says the narrator. "Even rectangles." ...
Movies (animation included) have always reflected larger society.
During the 20th Century, whatever was "okay" with the mainstream American culture (and fifty or seventy years back this meant white, Christian values), got put on screen. (The Jewish Louis B. Mayer made sure that Christian norms were on display in M-G-M films, because that's where the money was.)
Today society is shifting to same-sex marriage and cultures that aren's so 1950s America. Demographics are changing and culture along with it. Nothing is immutable. Laika's "Boxtrolls" is a reflection of that.