It's hard to put a definitive or accurate number on the percentage of citizens who were anti-Semitic during WWII and the Third Reich. Much of the population supported the Nazis, for varying reasons. Much of the population gave up their rights and, even if they were not anti-Semitic, were willing to watch and sit back while anti-Jew laws were enacted, their synagogues burned, and they were sent off to concentration camps because the Nazis, in their mind, were bringing back German glory and pride, as well as a better life.

Germany had been humiliated and devastated by the Treaty of Versailles that ended the First World War. A lot of Germans lived in denial that their armies had lost. Anti-semitism gained steam in the interwar period because many people preached that Germany had lost because of the Jewish people, and the Treaty of Versailles was a conspiracy by the Jewish and socialists. Anti-semitism had been prevalent in Germany since the 1800's, especially during the German Empire. While it did not have the success as it did during Nazism, anti-Semitism groups did try to gain power during Imperial Germany, and the German defeat and harsh consequences of WWI helped fuel anti-Semitism in Germany.

Even if much of the population was not anti-Semitic, the German people did not really speak out against it. There were not major riots and most people boycotted Jewish shops when told so and stood by during Kristallnacht, as well as when Jews were being shipped away. So, while it's hard to say how many Germans were anti-Semitic...... There was not a real effort to speak out against it and many turned a blind eye because their life and glory improved, even if they were not anti-Semitic. Also, those who spoke out against the Nazis were often persecuted, so fear could have also played a part. Keep in mind that, even if much of Germany may have held anti-Semitism ideals, they did not necessarily approve of the mass killings of Jews, if they knew about it.

So, while its hard to put a definitive number on the amount of Germans who were anti-Semitic, many, if not most, stood by and watched and did very little, whether they were anti-Semitic or not. It is possible there were other thoughts among the population, but they did not gain much traction. There were those who spoke out against anti-Semitism, of course, but it was not common among the population.

A good resource to check out is Richard J. Evans' "Third Reich Trilogy." Many historians feel it is one of the best histories of Nazi Germany available. It does have its problems, but it is a good resource on what you're wondering and the history of Nazi Germany itself. It covers extensively the history of anti-Semitism before and during the Third Reich, as well as other topics, causes of the rise of Nazism, and the history of Nazism and the Third Reich in general. Much of this response came from these books, and I think it would help you better understand anti-Semitism in Germany. There's a lot of background to it.