Actually the Croats divided during WWII. Some formed the Nazi-supported government of Ustashe Croatia, while others such as the Sisak Partisans fought under Tito along with most of the Serbs. The muslims, of course, sided with the Ustashe regime and with the Reich itself, the 13th Waffen-SS certainly being their largest and most visible display of support for Hitler but by no means their only. Mufti Husseini had all sorts of jihadi fascist organizations doing his dirty work in the Balkans during the war.
And of course, some Muslims joined Tito's partisan movement.
The fact remains is that the Christian and Christian/Heretic nations of Croatia, Germany, and elsewhere in central Europe made up the overwhelming majority of the Nazi Wehrmacht and all sorts of non-military fascist organizations doing Hitler's dirty work.
It's telling that the Nazis needed to use a foreign anti-Semitic cleric and the force of Christian Croatia's government to raise the 13th, while Christians and Heretics across Europe joined the SS in droves.