Jews had been living in Germany for much longer than there even was a Germany.
This is not right.
Julius Ceasar was the first to call the region east of the Rhine Germania, this was before 44BC. The first Jews came to Germania at the end of 1AD. Back than the Netherlands and the Flemish and German part of Belgium also belonged to it but besides that it was the Germany we know today. The first Jews probably hadn't much trouble here because the Germanic Tribes (and Nordic ones) where not really barbarians like people assume they were. If you learn more from the Germanic and Nordic Mythology you'll realize it is a beautiful and useful faith (and I say this as an atheist). Maybe faith is a wrong name it was more some kind of wisdom that they told to each other from generation to generation. One of the things it said was to be good for strangers, and that those strangers had another god wasn't really a problem, because you had the freedom to choose your own favorite gods, and people back than didn't hate each other because you worshiped Wodan and your neighbor Freya. This eventually let to the destruction of a big part of our culture when Christianity came in like the Trojan horse.
But when the name already existed (and the people and culture actually already existed way back before that) Judaism was still something from the desert.
Not that this all doesn't make your reasoning correct, the Jewish restaurant owner has the freedom to choose who he serves and who not. And the people against it who seem to be very pro the German people, should actually maybe learn their (own?) culture. Because freedom is in our genes but knocked down by faith and governments who want to control us, our ancestors would disapprove to force someone to do something he doesn't want, even if he worships a god we have no connection to. We should fight for our freedom, and freedom isn't something you can throw in the ring when it's beneficial for yourself. It is something that always should be applied, even for the people you don't like. As long as you don't harm anyone, you should do what you want, the Jewish person doesn't harm anyone if he doesn't serve the skinhead, the skinhead can eat somewhere else.