This is an interesting thread, because those who defend the pilot cite the fact that he is being pulled under by "politics" yet they fail to see that it was the pilot's decision to make a political statement with his machine, an unsafe one at that, that lead to the need for punishment.
If you are in the US Military, you are punished if you attend a political rally in uniform, as you must not estabish a link between the service and that political statement. You can most certainly attend such a rally in civilian clothes, of course.
This pilot chose to use his machine and crew to make a political statement, a strong one! Switch venues to test that statement, tearing down a US flag at a construction site could cause you to become an off ramp on the Brooklyn-Queens Exressway!
If the guy had been the employee of any company I know, and had done as stupid a thing, he would have been fired. Had he done it in his private helicopter, the CAA/FAA would have nailed him for safety violations, too (Open air assembly, flying too close, reckless operation, where do I stop?)
As far as the commander being to blame, that is pure bunk. The rules the pilot must follow are vast, but just to start, I'll bet he did not file a performance planning chart for that flag-pole stunt, now did he?
If we want to blame commanders, let it run all the way up to the top, where that pilot and 140,000 other very loyal troops were put into mortal danger, and 10,000 innocent Iraquis killed, for the imminent danger and immediate threat of totally ficticious WMD.