It's called "Blowback". In order to prevent another 9/11/2001 or worse, it seems important to understand the motivations behind the first one (I'm using the year to distinguish from the US-supported 9/11/1973 coup in Chile). Like you, I also doubt the Saudi government had anything to do directly with funding that 9/11. In fact, that 9/11 seems more a protest against the Saudi government by Saudi citizens, but with the protest directed at the perceived source of funding for the Saudi government by the USA. Let's turn the political situation around hypothetically to try to understand the emotional aspect of it better, imagining what it might be like if the Saudi government was meddling directly in US affairs.
Here is a first cut at trying to understand the social/psychological dynamics of the situation from a different perspective. Imagine Saudi Arabia somehow was sending billions of dollars of campaign donations annually to the USA to keep in power an oppressive administration in the USA (passing laws forcing all US women to wear burkas, only allowing males with brown eyes to hold public office or get university degrees, and with capital punishment on suspicion of premarital sex or homosexuality). Also, imagine that there were millions of Saudi soldiers stationed in US states to ensure a flow of manufactured goods to Saudi Arabia despite strikes and other unrest in the USA and nearby countries. Also imagine that the Saudis were also funding Japanese people who, from fear of earthquakes and tsunamis in Japan, had moved to Canada, bought a lot of the land, claimed a right to govern all of Canada because some Japanese people had moved to Canada 10,000 years ago across the land bridge from Siberia, and then forced most non-Japanese Canadian citizens in all of Canada to flee to the USA and were killing non-Japanese Canadians who remained and resisted the Japanese occupation. If you are a US citizen in such a hypothetical world, would you be at all upset by such a situation whatever your eye color? Imagine that some very upset and frustrated young US citizens decide to protest this situation by attacking some big buildings in Saudi Arabia by hijacking airliners to show how unhappy they are with Saudi government foreign policy and to show how they felt their hopes and dreams for a good life in the USA had been thwarted by Saudi meddling in US government. Imagine this attack is then used by Saudi Arabia to justify invading Mexico (where some of the hypothetical American hijackers trained) and Brazil (because it is claimed by the Saudis to have WMDs that hypothetical young Americans might use against Saudis). Imagine the Saudis then start supplying "intelligence" to the US government from listening to all US telephone calls about specific US citizens who might be unhappy about the situation and perhaps plotting unrest in the USA or planning more blowback against the Saudis.
Now flip this scenario around and back to reality (US funding Saudis and Israel and US troops in the Middle East) and does the fact the almost all of the 9/11 hijackers were frustrated young Saudi men make more sense?
Soon after 9/11 I saw an analysis in a magazine (maybe the Atlantic or New Yorker) of why the hijackers did what they did. I have not seen many such articles since. The point made there was that these were mostly young men whose hopes for significant advancement in Saudi society had seemed thwarted and they were led to blame the USA for that, because the USA was propping up the Saudi regime and otherwise meddling in the Middle East. Of course, being promised eternal bliss in "paradise" for becoming murderers can not be ignored as a related aspect of religious fundamentalism (including outrage about the occupation of Palestine), so there are layers of complexity here for that and other reasons. The motivations of the hijackers themselves may also be somewhat different than the motivations of the organizers at higher levels.
"The hijackers in the September 11 attacks were 19 men affiliated with al-Qaeda, and 15 of the 19 were citizens of Saudi Arabia. ... "
"The 9-11 Commission held its twelfth and final public hearing June 16-17, 2004, in Washington, DC. On June 16 the Commission heard from several of the federal government's top law enforcement and intelligence experts on al Qaeda and the 9-11 plot. It was at this hearing that the question "What motivated them to do it?" was finally asked. Lee Hamilton, vice chair of the 9/11 Commission said, "I'm interested in the question of motivation of these hijackers, and my question is really directed to the agents. ... what have you found out about why these men did what they did? What motivated them to do it?" The agents looked at each other, apparently not eager to be the one to have to say it. FBI Special Agent Fitzgerald stepped up to the plate and laid out the facts, "I believe they feel a sense of outrage against the United States. They identify with the Palestinian problem, they identify with people who oppose repressive regimes and I believe they tend to focus their anger on the United States." But this testimony was kept out of the 9/11 Commission Report and no recommendation was given to address the main motive for the 9/11 attacks."
So, it was not so much that "they hate us because we were free" (although there were some religious aspects of that). It was more that "they hate us because we fund their oppressors". Granted, there are additional layers of complexity including from religion and economics, but that is part of the bigger picture.
To bring this back to the source original article, it says: "The report also notes the MOI's use of invasive surveillance targeted at political and religious dissidents. But as the State Department publicly catalogued those very abuses, the NSA worked to provide increased surveillance assistance to the ministry that perpetrated them."
So, the USA is left in a difficult situation. Saudi citizens who resent their oppression or other treatment by a government propped up by US support still have reason to dislike the US government. But, if the US government does not help the Saudis via the NSA identify and suppress dissenting Saudi young men, then another 9/11/2001 becomes more likely in the short term, even as such a disaster or much worse becomes more certain in the long term if the USA continues to support a repressive Saudi government and otherwise take sides in Middle Eastern politics. What is the morally and politically correct solution to this dilemma? What policies should a US citizen now support? It's the kind of situation best avoided (see George Washington's farewell address which warned to avoid entanglements in foreign affairs) but it is too late for that. Also, to get to a good resolution, we have to acknowledge the truths behind the conflicts, but often conflicts include suppressing or spinning relevant details like misleadingly claiming "they hate us because we are free".
One thing I feel strongly is that given the increasing power of WMDs including bioweapons, the margin for political error grows smaller and smaller. Given that increasing risk, oppression does not seem like a good long-term strategy to ensure peace and prosperity in the 21st century. So, I feel we need to move instead towards some sort of transcendence of these 20th century (and earlier) conflicts. That included rethinking security to be mutual and intrinsic, like I mention here:
But others have been saying similar things for a long time:
And maybe we could create better software tools to help resolve such conflicts in a healthy way? As I suggested three years ago:
"This suggestion is about how civilians could benefit by have access to the sorts of "sensemaking" tools the intelligence community (as well as corporations) aspire to have, in order to design more joyful, secure, and healthy civilian communities (including through creating a more sustainable and resilient open manufacturing infrastructure for such communities). It outlines (including at a linked elaboration) why the intelligence community should consider funding the creation of such free and open source software (FOSS) "dual use" intelligence applications as a way to reduce global tensions through increased local prosperity, health, and with intrinsic mutual security."