There are clear rules in English and Chinese. English is absolute so "yes" means I am. Chinese is an echo language so "是的" means you are correct that I am not.

However, I do see Chinese making mistakes in English and English speakers making mistakes in Chinese and I am not 100% free of the guilt.

In the question "你不是犹太人吧？" there is already a "是“ in it, so a native speaker would use "对“ or "没错“ instead of "是的". They all means "correct" but by avoiding using "是" again, the chance of misunderstanding is minimized.