For a while now, I have grappled with this question. Not that it has shaken my faith per se, but I have struggled to come up with an adequate response to those who might find the question a tricky one themselves.
I think I've found the answer, thanks to a very good resource I stumbled upon, God Questions? I found its response to one of Atheism's favourite attacks on faith a very balanced and intelligent one: Why doesn't God heal amputees? Obviously, there is bound to be a counter argument, but some people will never accept the truth however challenging (or obvious) it might be.
Suffering, pain and healing are always going to be a stumbling block for many, but what this article helps me to bear in mind when faced with these difficult questions is the eternal perspective of things. Our life in this world is temporary - so is all the hurt, pain and sadness (as well as the joy, happiness and pleasure). We are eternal beings, with a life in heaven to look forward to.
Of course, we should value our present life and live it to the full - but not hold too tightly to it, remembering our ultimate destination.