That's a provocative and potentially controversial position for him to take, but it's decidedly not the same as advocating or in any way supporting any of the popular conspiracy theories. Paul's views still fall within the political norm and they don't in any way endorse any alternate interpretation of the basic facts of the events of 9/11.
Because there is this common perception among his own supporters that he holds beliefs which he seems not to, he ends up being asked about it a lot. Those supporters are delusional, so they pretend his answers denying their movement don't exist and for his part, Paul seems puzzled and annoyed that the rumors persist, as you can hear in this radio interview:
Paul has even rejected 9/11 conspiracy theories in a presidential debate, early in the 2008 election. But in this case, as often happens, when offered an opportunity to speak directly to his supporters and urge them not to continue to promote delusional ideas which hurt his candidacy dy association, his natural inclination to support free thought and free speech lead him into the error of appearing tolerant of their beliefs. Despite having every reason to whack them on the knuckles and send them to bed without dinner, he's too tolerant and too nice a guy to be firm with them, even if it may well cost him the presidency again in 2012 as it did in 2008.
A lot of this is a function of wilfull denial of reality, a kind of cognitive dissonance where the truthers are absolutely divorced from reality. In this video truthers ask him about the conspiracy and he gives a reasonable and compelling explanation for why their theories are irrational, because the government is too inept to have actually carried out a conspiracy on that grand scale, and that if anything went on it was just a coverup of government incompetence.
Clearly some people get the mssage, but a core group among his followers won't accept the truth about 9/11 even from a revered leader like Paul. The response you can see on the message thread which goes with the video shows how delusional his truther followers are. One writes "yeah sure.. he can't say it was a total inside job even though IT WAS. You have to be cautious about these harsh comments." Another rationalizes away Paul's statements saying "I think Paul suspects that it was an inside job too, but he doesn't want to cross that line, for it would completely ruin his presidential aspirations."