Are you sure you want to rotate the Pango context? I believe that functionality was introduced in the pre-Cairo days; now you would just rotate the Cairo context, like:
cr->save();
cr->rotate_degrees(90);
Glib::RefPtr<Pango::Layout> y_axis_label = this->create_pango_layout("y-axis label");
y_axis_label->set_font_description(font);
cr->move_to(...); // wherever you wanna put it
y_axis_label->show_in_cairo_context(cr);
cr->restore();
If you still don't see anything, make sure you are not moving the label out of the visible area.