Yep, there is some hostility towards bikers in Germany, but I wouldn't let that stop me from going there. There is also some hostility towards foreigners, but same in France. It's not common and you are just as likely to run into your average pig-headed so-and-so that is unfriendly for other reasons (or none at all...).
The real problem in these two countries is over-population (people and cars). The roads are often permanently clogged. Both can still be enjoyable on bikes, though: stick to the small roads and take your time. Avoid big cities and their surroundings and main roads leading to/from them.
France is less populated and so it's easier riding. Plus the climate is nicer, particularly in the South-East, where I have lived the last 7 years.
If I had to do this route and had the time I'd go via France: Alpes-Maritimes, Haute Provence, Vercors, Jura, Vosges, then perhaps through the SW corner of Germany and Belgium to the ferry.