I think it's partly because when spelling was standardized in the 17th-18th century, it was done with a "learned" view that spelling should reflect a word's origin. So you get "doigt" for finger because of the latin digitus, the circumflex to denote an S that has become silent (hôpital vs. hospital), and even overcorrections (that have been recorrected since), like nénuphar -> nénufar (ph is used to denote places where there used to be a greek phi, but nénufar comes from Arabic)