The persecutions were aimed at Jews and not Christians, because they were a result of Nazi racial politics and thus the Jews, much like Gypsies and, to lesser extent, Slavs (depending on which version of Generalplan Ost you consider to be true) were based purely of the 'race' (ethnic ancestry) rather than any professed religious or cultural affiliation. The Law for the Protection of German Blood and German Honour (one of the so-called Nuremberg Laws) based their definition of Jews on the ethnicity of parents and grandparents, with an additional provision, that people 'of mixed race' (Mischlinge, i.e. those having one or two Jewish grandparents) who are members of Jewish religious communities have to be treated as Jews. The specifics of the religious doctrine or customs were not important here and there is little that would suggest that Hitler or any high-ranking NSDAP officials actually possessed any knowledge about religious matters.

German National Socialists cannot be described as 'Catholic' by any stretch. First and foremost, the membership or support of the NSDAP was quite widespread and thus more or less uniform across confessions. Thus, as Germany has a similar number of Catholics and Protestants (the actual numbers might have varied from Land to Land), this was reflected in the religious composition of the NSDAP. But this point is largely moot, as the party as such was ideologically strictly materialistic and thus shunned any form of religion. More radical members, especially associated with SS, were openly opposing any form of organized religion, especially Christianity they considered a 'Jewish-influenced religion not suitable to the New Man'. Hitler himself said on numerous occasions that he cannot envision co-existence of any religion and the National Socialism, while Heinrich Himmler openly stated that one of the goal of the Nazi Party is to eradicate Christianity in Germany. This stance was particularly strong in case of Catholic Church that, unlike smaller Protestant denominations, was a powerful, international organization and thus was considered a possible obstacle in establishing a totalitarian rule over the Germany. Although reluctant to attack Catholic Church or its hierarchy openly (this did not apply to annexed territories, predominantly largely Catholic Poland), Hitler tried to weaken it by various means, e.g. dissolving various political and social organizations tied with the Church, such as Centre Party or Katholishe Junge Gemeinde (Catholic Boy Association) and its distaff counterpart, Katholische Frauenjugendgemeinschaft. Nazis also first censored and later completely banned the Catholic press in 1941, and were suppressing the Catholic schools so that in 1939 all such establishment were either dissolved or transformed into fully secular facilities. Christian welfare programs were also severely restricted an non-compliant with new racial policies. The feeling was mutual, and many clergymen (not only Catholic) were criticizing the NSDAP since the very beginning, focusing on blatantly secular and anti-Christian policies.. This culminated in the issuance of the Mit brennender Sorge encyclical by Pope Pius XI, criticizing the German policies and stating that the nationalism in Germany took the form that is nothing short of idolatry.