According to the Washposts account of Fight 93 Cheney did order it shot down, it was only till later that they determined it had crashed on it's own.
And, honestly.. it makes no difference one way or the other. The plane had to come down and the passengers knew that, as well as the Vice President.
You cannot allow someone flying a bomb to reach a target like the WTC, it's common sense. So, even if it was a shootdown how does this tarnish the Administration? Because they realized the same thing the passengers did? What does that prove and how is it bad?
That's my take on it. No matter who is President, if there is a terrorist threat, like what came to fruition on 9-11, the safety of thousands/millions must come first. I do think it is reprehensible for them to make some sort of scandal of such a gut-wrenching decision.