As a butcher, I was told it came from the same etymology as "butting" someone with your shoulder. As in - (hitting someone with) the end of something.

EDIT: the funnier etymology is with Beef. A beef shoulder is called a "Clod", literally because it's a big messy hunk of meat.

haha, in an agriculture class decades ago, when i learned the "boston butt" cut of pork was part of the shoulder, i used a memory aid to recall it on the exam. it was something like "people from boston can't tell a face from an ass."