>I'm trying to find a story in Iraq and Afghanistan where they shot down a hellfire missile with small arms.

No one is saying that, however the missiles have operators (who are human) and the operators have friends and families (who are human). The missile isn't what an efficient or effective guerilla would target.

>How will you fight the US Navy parked a good 200 miles off the coast and launching a tomahawk to blow up a neighborhood full of "rebellions" during this hypothetical Civil War?

Are you actually stating that you believe the US Government would indiscriminately level civilian neighborhoods using missiles during a hypothetical civil war? And if so, are you indicating that you would support the actions and legitimacy of said government?