That's a question I found myself asking God alot in the early months after my son's autism diagnosis. I think it's a question we ask of God any time something goes "wrong" (a.k.a not according to our plans).
I found this interview with Kempton Turner, a pastor at a church in Minnesota, where he talks about God's purposes in disability. His answers are the same I've come to after several years of wrestling over the question of "Why?" I hope it will be an encouragement to you today.