That comment was downvoted for engaging in a tired debate which had already been resolved to everyone else's satisfaction. The prior for "The U.S. government will intentionally murder thousands of its own citizens in a fake terrorist attack" is very low; the abundant evidence (including hundreds of eyewitnesses) that, y'know, planes crashed into the towers makes it even more unlikely. One piece of cherry-picked evidence against the obvious facts was obviously insufficient to change anyone's opinion (furthermore, it wasn't even the point of the post), so it was downvoted.
For the same reason, I downvote "evidence" presented for various religions. The issue has been decided; no given piece of evidence is going to change anyone's opinion, and rehashing the issue is a waste of everyone's time. Political incorrectness has nothing to do with it.
People who go back and downvote every post or comment a Less Wrong user has ever made, please, stop doing that. It's a clever way to pull information cascades in your direction but it is clearly an abuse of the content filtering system. It's also highly dishonorable. If you truly must use such tactics then downvoting a few of your enemy's top level posts is much less evil; your enemy loses the karma and takes the hint without your severely biasing the public perception of Less Wrong's discourse.
(I just lost over 200 karma in a few minutes and that'll probably continue for awhile. This happens to me every few weeks. Edit: I mean it's been happening every few weeks for a few months for a total of only three or four. Between 400 and 700 karma lost total I think? I don't mean to overstate the problem.)