That's a good question.
For every verse or prophetic saying or tradition that can be misinterpreted or misunderstood, there is always another one that can act as a counterbalance to show that the misinterpretation and the misunderstanding is not correct. Anti-Semitism, of course, is wrong, and as you correctly pointed out, it's not coming from the Quran. Also, even if someone were to look at the prophetic teachings, there would be a number of examples of cordial and positive relations with Jewish people.
I think it's those types of teachings that have to be shared and disseminated. That's one thing we try to do, especially when there is an issue that comes up. Many Canadian imams will tackle the issue head-on at Friday prayers and give an overarching view so that there are no misrepresentations or misunderstandings based on cherry-picking. Unfortunately, that's what radical extremists like to do, and haters as well. They like to cherry-pick, whereas the Islamic teachings are based on a compendium of teachings.