It's not the President's job to explain to the people how government works, that's the media's job. In a perfect world, the media would be doing it's job, but they're not, they're vested interest is to undermine this administration or any Republican administration in days past. When was the last time you saw the media question the White House when a Democrat occupied it? I can't ever recall a time. The media wants Bush to apologize, because that's what they've been trying to get him to do for everything he's done from the Oval Office for the last 4+ years.
It would be their justification that he's a bungler, unfit for office.
Respectfully, it's not the media's job. It is the responsibility of each American citizen to learn how the government works. The media can be a source of information, but it's still the responsibility of each citizen.
That being said, it is up to the President to get his message out. If a wrong message is getting out, it is up to him to go front and center to correct it.
Reagan had to deal with a hostile media and he found a way to do it. I believe that Bush is capable of doing it but for some reason just won't.