Judging from history, citizens of most countries don't particularly relish "hosting" foreign garrisons. So it should come as no surprise that when foreign troops misbehave, the response is inevitably disproportionate. Americans taken aback or offended by the recent protests in Okinawa would do well to recall their own nascent nation's reaction when they were "host" to British forces.
The U.S. fleet is not here to protect Japan, so let's please dispense with that cliched pretense. The Japanese public didn't invite the American military to protect them; instead, Japan became a de facto vassal state after losing the Pacific War. American bases were established here as a projection of U.S. military influence over the Pacific and as a counter to Soviet and Communist Chinese influence.
Sixty years of hosting American troops has not demonstrably made Japan any more secure. On the contrary, one could argue that North Korea, for example, would not be aiming nuclear weapons at Japan if it weren't for the U.S. presence.
So, as well meaning as most American troops assuredly are, they need to remember that as a foreign "guest/occupying" force, they are held to a different standard.