If you read the article from The Atlantic in the OP, it's clear most of the danger to Jews in Europe is coming from Muslims. Here are some quotes from the article.
But what makes this new era of anti-Semitic violence in Europe different from previous ones is that traditional Western patterns of anti-Semitic thought have now merged with a potent strain of Muslim Judeophobia. Violence against Jews in Western Europe today, according to those who track it, appears to come mainly from Muslims, who in France, the epicenter of Europe’s Jewish crisis, outnumber Jews 10 to 1.
On the morning of March 19, 2012, a man named Mohamed Merah, a French citizen of Algerian descent, parked his motorbike in front of the entrance of a Jewish school in Toulouse called Ozar Hatorah, which is in a placid residential neighborhood not far from the city center. Merah, who had been radicalized in a French prison and trained in an al-Qaeda camp in Pakistan, dismounted and almost immediately began firing a 9 mm pistol at students and the parents who were dropping them off. He killed a 30-year-old rabbi and his two sons, who were 3 and 6 years old. Merah then walked into the schoolyard, shooting at students. He chased down an 8-year-old girl named Myriam Monsonego, catching her by the hair. Merah held her down and placed his 9 mm to her head, but the weapon jammed. He switched to another handgun, pressed it against her head, and fired. The sound of shooting had brought the school’s principal to the school yard. Yaacov Monsonego arrived to see Merah execute his daughter.
There are more details in the article about Muslim children in Toulouse who tell their parents not to go to a Jewish doctor.
Like many of the banlieues that ring Paris, Montreuil bears no socioeconomic or aesthetic resemblance to the Paris of popular imagination. The architecture is rude, the parks are unkempt, and the people, many of them immigrants from North Africa, are estranged from la belle France. On the way to Montreuil, in the Métro, I passed defaced posters of the musician Lou Reed. Stars of David had been drawn on his nose. Other graffiti was less ambiguous: Nique les Juifs—“Fuck the Jews.”
The students I talked with in the library generally agreed that their future lay outside of France. “A lot of the Muslims hate us here,” a student named Alexandre said. His parents had already moved to Israel. They were two of the roughly 7,000 French Jews who left for Israel in 2014. Alexandre would be joining them after graduation.
The students talked about ways in which Jews concealed their identity. I’d heard that it had already become fairly common practice in some of the apartment blocks in the banlieues for Jews to remove the mezuzot from their doors. A mezuzah is a piece of parchment that contains Bible verses and that is placed in a case and then affixed to a doorpost. In some suburbs, mezuzot had become pointers for those in search of Jews to harm.
But the students told me something new. “Jewish people are telling other Jews to take down their mezuzot,” one of the students said. “People are being pressured to hide that they are Jewish. The pressure can be very intense.” The impetus for this new campaign seems to have been an incident that occurred in early December, in which a group of robbers broke into an apartment in Créteil. They told the occupants that they knew they were Jewish, and therefore wealthy, and then they raped a 19-year-old woman in the apartment.
Malmö, which sits across the Øresund from Copenhagen, has a population of roughly 300,000. This includes a large number, perhaps 50,000 or so, of Muslim immigrants. The Jewish community is much smaller—by some estimates, there are fewer than 1,000 Jews; the population has dropped by half in recent years. Malmö’s leadership has at times been at odds with Malmö’s Jews. A former mayor said that the city accepts “neither Zionism nor anti-Semitism”—a statement that was taken as hostile by Jewish Swedes supportive of Israel’s existence.
Acts of anti-Jewish harassment and vandalism are common in Malmö, and Kesselman is a main target, because he is the only Jew there who still dresses in an identifiably Jewish manner—kippah, black hat, black coat, and long beard. Jewish teenagers in Malmö told me that wearing a Star of David necklace can incite a beating. Kesselman estimates that he has been the target of roughly 150 anti-Semitic attacks in his 10 years in the city, mainly verbal, but also physical. “There is a lot of cursing at me, and people sometimes throw bottles at me from their cars. Someone backed up their car in order to hit me,” he said when I met with him. Occasionally, he said, people spit on him.
I spent one afternoon interviewing people in the main shopping mall of the Rosengård district, which is predominantly home to immigrants. Several of the Muslims I interviewed expressed benign feelings toward Jews. They knew of Malmö’s reputation for anti-Semitism, and regretted it. A couple of others expressed objections to Israel’s existence, but absolved “the Jews” of collective responsibility. But more common was conflation, and exaggeration. I asked several people to tell me where they find information about Jews and Israel. Television stations such as Al Jazeera and the Hezbollah station, Al‑Manar, were cited, as was the preaching of Scandinavian imams. One Danish imam, Abu Bilal Ismail, became famous last year for urging worshippers in a Berlin mosque to kill Jews: “Count them and kill them to the very last one. Don’t spare a single one of them.” He later explained to a Copenhagen newspaper that he “never meant all Jews.”
One man, an Iraqi refugee, told me, “The Jews have too much power everywhere.” Another man, of Sudanese background, explained that the Koran itself warns Muslims to fear double-crossing by Jews. “They killed the prophets and tried to poison the Prophet Muhammad,” he said. I did not hear critiques of Israel’s occupation policies. I heard, instead, complaints about the Jews’ baleful influence on the world.
When I left, two policemen were patrolling the narrow street outside the museum. A temporary surveillance post had been erected just across from the entrance. I asked one of the officers whether this level of security was normal. He said the government had increased security around the museum last spring, shortly after a massacre at another Jewish site: On May 24, four people were murdered at the Jewish Museum of Belgium, in Brussels, allegedly by a French Muslim of jihadist bent named Mehdi Nemmouche. Two Israeli tourists, a French volunteer, and a Belgian employee of Muslim and Jewish descent were killed. Nemmouche had recently returned to Europe after a term with ISIS in Syria, where, according to a former French hostage of ISIS, his specialty was torturing prisoners.
Valls is deliberate and—unusual for a French politician of the left—blunt in identifying the main culprits in the proliferation of anti-Jewish violence and harassment: Islamist ideologues whose anti-Semitic and anti-Western calumnies have penetrated the banlieues. But he goes further: France’s “new anti-Semitism” is also the product of what he understands to be a malicious sleight of hand on the part of Israel’s enemies to repackage anti-Semitism as anti-Zionism.
According to the Community Security Trust, 2014 saw the highest number of anti-Semitic incidents in the United Kingdom, which is home to 300,000 Jews, since the organization began its monitoring efforts, in 1984: it recorded 1,168 anti-Semitic incidents. This is more than double the number of incidents in 2013, and exceeds the previous record, from 2009, of 931 incidents. In a recent survey conducted on behalf of the Campaign Against Anti-Semitism, a quarter of British Jews said they had considered leaving the country; more than half of those surveyed said they fear that Jews have no future in Great Britain.
Cameron condemned demonstrators who took out their frustrations with Israel on Europe’s Jews. I asked him whether there existed in his mind a bright line that separates anti-Zionism from anti-Semitism. He answered: “I think it is unfair and wrong to lay at the door of Jewish communities of Europe policies pursued by the government of Israel that people might not agree with—just completely wrong.”
He went on to say: “As well as the new threat of extremist Islamism, there has been an insidious, creeping attempt to delegitimize the state of Israel, which spills over often into anti-Semitism. We have to be very clear about the fact that there is a dangerous line that people keep crossing over. This is a state, a democracy that is recognized by the UN, and I don’t think we should be tolerant of this effort at delegitimization. The people who are trying to make the line fuzzy are the delegitimizers.”
Later in the article there are quotes from Marine Le Pen, the leader of France's National Front Party. They're often classified as a neo-Nazi party. I don't know enough about French politics to know to what extent that's true and to what extent it's propaganda. However, what is clear is that the National Front talks about defending Jews in France, and they don't deny who is the danger to Jews in France. To their credit, the mainstream French parties (including the ruling Socialists) did a good job of talking about defending Jews in France after the massacres in January. I tend to suspect this was partly out of fear that the French people might actually vote from the National Front.
If you are someone whose main goal is to prevent parties like the National Front from coming to power (rather than protecting Jews), then I can understand why you'd be dishonest about who is attacking Jews. It would make sense to try and blame it on "right-wingers" instead fo radical Muslims. It takes a real blindness to believe that the danger is actually from "right-wingers" instead of Muslims.