Problematic passages in the Quran?

How do I go about making sense of those rather "daunting" passages in the Quran? It is said that the Quran applies to all times—meaning that God provided guidance relevant for every era, whether in the past or today. Critics of Islam often seize upon passages like "and kill them all" to undermine the faith. To be honest, however, I also find these passages unsettling and wouldn't know how to explain them. I want to embrace the faith as a whole, but it isn't easy.