In the case of 9/11, there are a lot of things that are not "factually disproven", because they aren't science based questions.

Everyone jumps on the joke about "Jet fuel can't melt steel beams" as being a cornerstone of every 9/11 "truther", which is completely unfair. There are lots of people who question 9/11 who fully understand that temperatures from burning fuel weakens steel.

People don't deny 9/11 happened (ok, most people...), people question what the motivation was, whether the US was involved in the attack, etc. These are all reasonable things to ask.

Personally, I still have questions, such as why did building 7 collapse when nothing else in the area did, and when it conveniently was a secret service and CIA building. The Report even states that it's the first time a building over 15 floors collapsed due to fires caused by burning office equipment. I'm not a moron, I can recognize that the 9/11 plane attacks were not fake, or at the very least, more plausible than any other method of collapse. That doesn't mean that looking into why it happened, who was involved, what information is being hidden, etc are not worthy endeavors.

There is nothing inherently wrong with conspiracy theories. Look at Snowden. For a very long time there was many people who believed the government was spying on US citizens. If they had a subreddit would they have been banned/quarantined? Questioning the government is a good thing, you'd think that would be more apparent now than ever, especially here on Reddit.