Specifically, see below...
STEPINAC'S PERSONAL CULPABILITY
As archbishop of Zagreb and military vicar to the armed forces and the Ustashe, Stepinac was the de facto head of the Catholic Church in Croatia during the Second World War. In a regime that counted its Catholicism as the core of its national identity, the Archbishop's importance and influence in the events that transpired there during and after the war were substantial.
There is no question that he initially welcomed the establishment of the Ustashe state as the fulfillment of centuries of Croatian aspirations for independence. In a pastoral letter published less than a month after the founding of the NDH, Stepinac consecrates and legitimizes the new regime:
For as confused as today's fateful events may be, as varying as the factors may be that have influence on the course of events, one can nonetheless see the working of the divine hand.
He likewise lauded the enactment of Catholic dogma into law that marked the initial stages of the regime. He looked with particular favor on laws that meted out the death penalty for abortion and 30 day in jail for swearing. There is no doubt either that he welcomed the elimination of religious tolerance. In a diary entry that details his first meeting with the poglavnik Stepinac notes with evident approval the coming suppression of rival faiths.
The Archbishop gave his blessing for his work.... When the Archbishop had finished, the poglavnik answered that he wanted to give all his help to the Catholic Church. He also said the would uproot the sect of Old Catholics which was nothing more than a society for divorce. He went on to say that he would not show tolerance toward the Orthodox Serbian Church because, as he saw things, it was not a church but a political organization. All this left the Archbishop with the impression that the poglavnik was a sincere Catholic and that the Church would have freedom of action, even if the Archbishop did not delude himself into thinking that all these things could happen easily.
The religious intolerance of the Ustashe continued to be a major factor in Stepinac's support for the regime throughout the war. At one point, he complained bitterly that the Italian fascist troops that were occupying a portion of Croatia during the war were allowing so much religious freedom that it was threatening the stability of the state. To the Bishop of Mostar Stepinac wrote,
The Italians have returned and resumed civil and military authority. The schismatic Churches have immediately come to life again, and the Orthodox priests, in hiding up till now, have reappeared in freedom. The Italians seem to be favorably disposed toward Serbs and severe toward Catholics.
He addressed a similar complaint to the Minister for Italian Affairs at Zagreb:
It so happens that in the Croatian territory annexed to Italy a constant decline in religious life is to be observed, and a certain discernible shift from Catholicism to schism. If that most Catholic part of Croatia should cease in the future to be so, the blame and the responsibility before God and history will lie with Catholic Italy. The religious aspect of the problem I am discussing makes it my duty to speak in such plain and open terms, since I am responsible for the religious well-being of Croatia.
Stepinac also explored the possibilities for enriching the church at the expense of its dispossessed Orthodox rivals. The Archbishop specifically petitioned the poglavnik to hand over the Orahovica Serb monastery to Trappists whom Hitler had expelled from their monastery at Reichenberg. http://www.pavelicpapers.com/features/essays/psg.html