One of the biggest assumptions Ron Paul's detractors seem to make is that America and the American people are somehow one and the same. So when he puts forth the suggestion that our government is an indirect cause of attacks on us, it can be twisted as a "blaim the victim" mentality.
People also seem to equate Dr. Paul's idea that we shouldn't invade other countries or engage in any sort of warfare unless it is in response to a threat towards the United States seems to be equated to "isolationism". I can't quite grasp how sending off our military into the business of other nations is less isolationist than not doing so. Whatever good our military can do, it is ultimately a killing machine.
But, about the motives...
CIA analyst Michael Scheuer (I his wikipedia page coves his qualifications well) seems to think al Qaeda genuinly believes its complaints against us. Of course, he could be incorrect. Right or wrong, both he, the 9/11 commission report, and many others acknowledge that our government's actions in the Middle East are responsible for creating a vast number of al Qaeda's followers. The nuttiness of certain al Qaeda members is a problem, but there are nuts everywhere. The largest problem is al Qaeda convincing the muslim world that their views are correct, and there is little doubt that our foreign interventions in the Middle East have furthered that goal.
9/11 Commission Report said:
2.2 BIN LADIN’S APPEAL IN THE ISLAMIC WORLD
It is the story of eccentric and violent ideas sprouting in the fertile ground of political and social turmoil. It is the story of an organization poised to seize its historical moment. How did Bin Ladin—with his call for the indiscriminate killing of Americans—win thousands of followers and some degree of approval from millions more?
The history, culture, and body of beliefs from which Bin Ladin has shaped and spread his message are largely unknown to many Americans. Seizing on symbols of Islam’s past greatness, he promises to restore pride to people who consider themselves the victims of successive foreign masters. He uses cultural and religious allusions to the holy Qur’an and some of its interpreters. He appeals to people disoriented by cyclonic change as they confront modernity and globalization. His rhetoric selectively draws from multiple sources—Islam, history, and the region’s political and economic malaise. He also stresses grievances against the United States widely shared in the Muslim world. Heinveighed against the presence of U.S. troops in Saudi Arabia, the home of Islam’s holiest sites. He spoke of the suffering of the Iraqi people as a result of sanctions imposed after the Gulf War, and he protested U.S. support of Israel.
9/11 Commission Report said:
...America is also held responsible for the governments of Muslim countries, derided by al Qaeda as “your agents.”Bin Ladin has stated flatly,“Our fight against these governments is not separate from our fight against you.”14 These charges found a ready audience among millions of Arabs and Muslims angry at the United States because of issues ranging from Iraq to Palestine to America’s support for their countries’ repressive rulers.
Michael Scheuer seems to believe our actions have far more of a role in convincing the average Muslim of our evil than anything else mentioned in the 9/11 report.
Though, I should point out that Dr. Paul's objections to our military interventions pre-date 9/11. His objection is, ultimately, more pragmatic than just the recent terrorism problem. He simply looks at the past 50 years of history, looks at both Iraqs, Vietnam, Korea, etc, and believes that our foreign military interventions have done more harm than good to this nation and its ability to defend itself. They have, of course, also done both harm and good to other nations, but Dr. Paul seems to believe our government's role is to protect our nation first and foremost.
I'm not sure if he would equate our embargos on Japan's oil and scrap metal which led to our being attacked at Perl Harbor as an intervention or not. He seems to speak favorably of our enterance into WWII, so I'd imagine he has no argument against our enterance into it.
Why don't you care about this hypocrisy? 
