I have to admit, this one burned me too. The President IS the Commander in Chief and as such is entitled to use military transportation. I don't see how this is any different than him using Air Force One or his Marine Corp choppers.
On the other hand, risking a carrier landing may be questionable behavior. They are inherently dangerous and accidents are usually fatal. That was, IMO, an unwarranted risk. As the President of the US, and especially in times of crisis, he should remember that his first responsibility is to the people that elected him. Risking his life like that was irresponsible, IMHO. The taxpayers foot a huge bill to fund the Secret Service to protect POTUS, and then he risks his life for a photo op. Not too bright.