This interesting post at the Algerian Review quotes two letters sent by the Algerian liberation movement, the FLN, to the Jewish community, as evidence that Jews were not targeted for their religion. It was as French nationals that the Jews were assumed to be complicit with the pieds noirs. My comment follows: (with thanks: Sacha G.)
"Many suspected Algerian Muslims, Jews and Christians were targeted during the mob killings. Some Jews and Christians continued to live in the infant state even though the majority left. I do not believe that the FLN and the revolution had an inherently racist or xenophobic agenda. While digging through history books, specifically Mohamed Harbi’s La Guerre d’Algérie, published in 2004, I came through a letter from the FLN written to the Jewish community in 1962. The FLN tried to engage the Jewish community and appealed to them to side with the Algerian revolution. The FLN was sympathetic to the plight that the Jews suffered at the hands of the Nazis and Vichy’s government. It aknowledges the help of many Jews that were in the cause of the revolution. (...)
From the translation of the first letter (1956) (all emphasis is mine):
The National Liberation Front, which has led the anti-colonialist revolution for the past two years, feels that the moment has arrived when every Algerian of Israelite origin, in light of his own experience, must without any ambiguity choose sides in this great historic battle. The FLN, authentic and exclusive representative of the Algerian people, considers it its obligation to directly address the Israelite community and to ask it to solemnly affirm its membership in the Algerian nation. This choice clearly affirmed, it will dissipate all misunderstandings and extirpate the seeds of hatred maintained by French colonialism. It will also contribute to recreating Algerian fraternity, broken by the arrival of French colonialism.[...]
Without going too far back in history, it seems useful to us to recall the time when the Jews, held in less consideration than animals, didn’t even have the right to inter their dead, the latter being secretly buried during the night wherever this could be done, due to the absolute prohibition against the Jews having any cemeteries. At precisely this period Algeria was the refuge and land of freedom for the Israelites who fled the inhuman persecutions of the Inquisition. Precisely during this period the Israelite community was proud to offer its Algerian fatherland not only poets, but consuls and ministers.
It is because the FLN considers the Algerian Israelites the sons of our Fatherland that it hopes that the leaders of the Jewish community will have the wisdom to contribute to the building of a free and truly fraternal Algeria…
And from the second letter (1962):
The Algerian problem is at a decisive stage. We want to address this appeal to you, in the face of the hysterical and racist clamor of the fascists who claim to speak in your name, declaring that you are French and that you are all participants in the criminal acts of the backwards colonialists. You know full well that this is both a gratuitous declaration and a policy of mystification that should fool know [sic] one, and even less so you, who are Algerians.[...]
…Recently, in Oran, demonstrations provoked by young hotheads in the Israelite neighborhood took place, followed by fires set in stores belonging to Muslims. These acts are the clearest illustration of how some of you attempt to thoughtlessly align yourselves with the racial policies of the ultras. Will you today make yourselves the accomplices of the backwards colonialists by rising up against your Algerian brothers of Muslim origin?…[...]
Israelite compatriots, many Israelites are active in our ranks. Some among them were interned, others are still in prison for their acts in service to the Algerian cause. Algeria’s independence is near; independent Algeria will need you and tomorrow you will need it, for it is your country. Your Muslim brothers honestly and loyally offer you their hand for solidarity coming from your direction. It is your duty to answer.
These letters are not new, I am not trying to break new ground or rewrite history. They were just found by a curious mind digging back through the history of his country. These letters do not excuse the treatment that Jews or anyone endured after the revolution, what they show is that the Jews were not targeted because of their religion, they just shared the fate that anyone that was suspected of complicity and treason with the French did.
During the Algerian war the Jews tried to maintain a studied neutrality: at this time conciliatory letters were also written by the CJAES, the representative body for Algerian Jewry, declaring that Jews were against violence of any kind. Although some Jews did support the FLN, many were murdered by them, according to Les juifs d'Algerie, deux mille ans d'histoire by Ayoum and Cohen. The turning point came on 12 December 1960 when the Great synagogue of Algiers was ransacked and 'Death to the Jews', together with swaztikas, scrawled on the walls. The desecration of the Jewish cemetery at Oran soon followed, the stabbing of the hairdresser Choukroun and confrontations between Jews and Muslims. From then on, it is hard to argue that the Jews were not targeted qua Jews.
Although the new Algerian leader Ben Bella made an appeal to the Jews to stay on, the Jews had little option but to join the mass evacuation from Algeria of the French pieds noirs. In March 1963, Algeria passed its nationality code, effectively excluding any citizen who was not a Muslim by birth.
More on the Algerian Jewish community here