Looks like that's a bug in the library as in SVG lines are transformable. In the meantime you could use a path to create a line.
var s = Snap(600, 600),
line = s.path("M0 0 100 100"),
matrix = new Snap.Matrix().translate(100, 100);
line.attr({
stroke: "#F00",
strokeWidth: 4
});
line.transform(matrix);