There are a few things to keep in mind when it comes to anti-Semitism in the middle ages. For one, it isn't the same for the most part as anti-Semitism of the last 200 years or so. Rather than being attacked as a racial group most of the medieval intolerance was linked to understanding participants as religious groups.

Secondly, as is necessary to point out in any medieval question, the middle ages is a long time and society in 700AD was not the same as society in 1400AD. Most anti-Semitism of the like you're referring to starts to really increase in the late 12th century and 13th century. Prior to this you do have accusations of Deicide and anti-Semitism on an intellectual level, and localised popular violence during the first crusade, but popular violence really begins to escalate around 1200AD. For instance, there are records of this rise in anti-Semitic mobs and violence in the time of Richard I (1189-1199), who opposed such mobs on the grounds that it was an insult to him as King to target his Jewish subjects without his permission. Later monarchs would change this position culminating in the expulsion of Jews by Edward I.

To Christians, Jews had rejected Christ as their saviour and were responsible for his death. Accusations of Jewish Deicide, which held that all Jews have collective responsibility for the death of Jesus as well as panic about blood libel, host desecration and Satan worship inflamed Christians at this time. A common quote from the gospel of Matthew used to explain the origin of the concept of Jewish Deicide is below:

So when Pilate saw that he was gaining nothing, but rather that a riot was beginning, he took water and washed his hands before the crowd, saying, "I am innocent of this man's blood; see to it yourselves." And all the people answered, "His blood be on us and on our children!"

— Matthew 27:24–25

As for your mention of Martin Luther, I would highly recommend reading this answer by u/sunagainstgold which goes into detail on his anti-Semitism.

A central part of most denominations of Christianity is that Jesus was a prophesized Jewish Messiah and that all Jews (and non-Jews) should accept him and follow his teachings as well as acknowledge his divinity. To Christians, they are the *next step* and the logical progression of Jews. Most Jewish groups however, even if they approve of Jesus personally, will not regard him as the Messiah and will not accept the claims of his divinity.

So to these Christians of the medieval period while Jews from before the time of Jesus (like those in the old testament) may well be worthy of praise, study and retelling of their stories, Jews after the time of Jesus have deliberately chosen to reject Jesus. Mosaic law and traditions as well as the covenant were fulfilled by the sacrifice of Jesus and so keeping to those traditions and maintaining Judaism was considered anti-Jesus and thus blasphemous to Christians of the high and late middle ages. This led to rampant outbreaks of popular violence culminating in expulsions and pogroms.