Arguably originated in the German-French Elzas. Schaeffer means shepherd. Although a discussion is going on if it derives from the German 'Schafter' which would mean something like 'steward', but that could be a wish for ancestors of higher stature. The combination 'ae' (which derives from ä) and the double 'f' is a bit extra-ordinary, because the usually a single vowel precedes a 'ff' (or a single 'f' would follow 'ae').
In the Netherlands there are supposed to be to big 'clans', the catholic in the South and the protestant in the North.