Just as in every other country in the world, there are going to be those who find a particular religion troubling. France has its share of anti-Semites just as the US does. That said, the industrial regions of NE France, Marseilles, les Banlieus de Paris and of other big cities are probably the places to avoid and not strictly because of anti-semitism. You won't have a problem as a tourist unless you wear your religion on your sleeve.
I've found that cyclists get a lot of respect in France, much more than in the US anyway. Rural France is much more welcoming than is urban France but the same can be said for the US. I too would advise not doing the Riviera on a bike. It is packed with No. Europeans in the their cars in the summer and Provence might not be the best place either. The Rhine and Rhone valleys are great!
I've not been to Italy so can't advise on the differences. I am planning a trip through Croatia, maybe, this summer. Anyone been there?