My sons are both athiests by choice, so I can sympathize with your dilemma. I was raised by catholic parents who didn't have answers to my questions about the holes in their religion. Deep down I think, my Dad was agnostic. He was more understanding of me and allowed me to stop attending mass at 16. Part of that acceptance came at great expense to our family, though.
When I was 14, my 8 yr old brother drowned. My Dad had a crisis of faith after that, and had a lot of questions regarding god's "plan". Our parish priest came over the day after the funeral to talk to my parents. The only answer he could come up with to Dad's question of WHY? was "it's all part of god's plan for us, we aren't meant to understand the will of god". That wasn't enough for him. So, a few years later, when I asked to be set free from "playing along", he let me go.
Now, as an adult with children of my own, I can understand the agony they went through when Scott died. The church didn't have any answers, because there aren't any. It's human instinct to reach for something to believe in when you're in need, and it's a hard reality to face the fact that life sometimes sucks for no reason. But it gets better.
I'm not sure what I'm trying to tell you Emanuel, except to love your parents, despite your differences, because they love you more than life itself. They'll adjust eventually, it just takes time.