> Muslims often say: "Stop calling all of us terrorists and stop saying Islam encourages terrorism because you are missing the real underlying issues. We want everyone to be happy just like you do, but we think your understanding of terrorism is flawed."
So this is the context I am responding to, the hypothetical situation of a Muslim claiming the above.
> because, when you accuse someone of being a terrorist
No, I'm responding specifically to the "stop saying Islam encourages terrorism" part. When I say "Any time I've seen a Muslim actually talk about the issue, and explain how Islam doesn't encourage terrorism", I don't mean in the context of responding to an accusation of being a terrorist.
> You've decided that a religion is guilty and want individuals to show proof of innocence?
What have I decided about the religion? I implied that if it's true that Muslims are saying "you are missing the real underlying issues", then I've yet to see one attempt to explain.
Also, If I had decided that a religion is guilty, who else but individuals could demonstrate otherwise? Religion has no life of it's own, it exists only in the medium of the individuals who decide to carry it.