In the closing months of the war and immediately after, many were tried and killed by communist Partisans. Many were also killed without any trials in retributions. Most infamous is the major retreat from Zagreb to Austria (Bleiburg), as the retreat included also a large number of civilians. Thing to note here is, first that retreating Ustaše continued to wage war after Germany surrendered for at least a week more. Most of those that reached Austria were returned to Yugoslavia, in accordance with Yalta agreement. However, many, especially high ranking Ustaše, did escape. Their leader, Ante Pavelić, for example, died of old age in Spain, many settled in South America and Australia.

The way Yugoslav authorities prosecuted war criminals was not always legally solid. Many were killed outright, many more after short formal trials, many similarly sent to labor camps. Depending on their immediate involvement punishments than ranged from death, years of labor, or for most of those that didn't immediately participate in Ustaše crimes exclusion from public and political life.

I don't know why more isn't taught in schools about them. They are covered in Croatian textbooks, and I guess in Serbian as well. Outside ex-Yugoslavia they are perhaps just a too marginal a topic. In teaching history, especially 20th century, a rigid selection must always be made because of limited time available.