Heh, you have to laugh - a Tecnorati search for Stephen E Jones brings up a lot of results. The best one being the following from 'Right Wing Pundit':

Once a theory of moonbats and fringe groups, the professor's endorsement actually adds credence to such garbage.

This professor's endorsement of such a theory suggests that 9/11 was an inside job and greatly tarnishes the school's image.

[....]

Voice your concern to the university president here.

For a thorough debunking of 9/11 conspiracy theories, check out this article from Popular Mechanics. [my emphasis]
On a follow-up post he says

Here's my thoughts on the problem with BYU's Steven Jones and his publication of '9-11/inside job' conspiracy theories. This is taken from an email to BYU's president. I don't address the problems with Dr. Jones's arguments (which are not my expertise), and only briefly mention the problem with conspiracy theories in general (more about that in a later post). [again, my empahasis]
His entire 'argument' rests on the 'fact' that:

In an era of unprecedented anti-Americanism both at home and abroad, the publication of conspiracy theories implicating our government in the mass-murder of its own citizens adds fuel to the fire. Conspiracy theories take a lot of work to disprove, and even after a thorough debunking, they live on. Because of Dr. Jones's publication, even after someone goes to the trouble of once again disproving the claims of an 'inside job,' extremist websites and anti-American agitators will point to the original publication when they call our national leaders "murderers," "Hitler," and "war-criminal." BYU's name should not be involved with such deceit and hate.
Interestingly, the subtitle of his blog is "Encouraging ideological DIVERSITY, political TOLERANCE and EQUALITY of opportunity."

But on the comment section of the second article, he has deleted two comments, claiming they were 'spam'.

Like I said, you have to laugh.