Others have written very good rebuttals of the paper, which is more in line with neo-Nazi and modern Iranian thought than reality.
"The combination of unwavering U.S. support for Israel and the related effort to spread democracy throughout the region has inflamed Arab and Islamic opinion and jeopardized U.S. security. ... Why has the United States been willing to set aside its own security in order to advance the interests of another state?... The explanation lies in the unmatched power of the Israel Lobby. Were it not for the Lobby's ability to manipulate the American political system, the relationship between Israel and the United States would be far less intimate than it is today.... AIPAC, which is a de facto agent for a foreign government, has a stranglehold on the U.S. Congress.... manipulating the media... Pressure from Israel and the Lobby was not the only factor behind the U.S. decision to attack Iraq in March 2003, but it was a critical element....the United States has a terrorism problem in good part because it is so closely allied with Israel...Viewed objectively, Israel's past and present conduct offers no moral basis for privileging it over the Palestinians...Israel and its American supporters want the United States to deal with any and all threats to Israel's security. If their efforts to shape U.S. policy succeed, ...Israel gets a free hand with the Palestinians, and the United States does most of the fighting, dying, rebuilding, and paying."
I would like to mention one one minor point that easily destroys the entire premise of the paper, that if the US would stop supporting Israel then the world's Arabs and Muslims would have no problem with America.
Was there any European country that was more sympathetic to Palestinian Arabs than Denmark? Was there any Western nation that allowed Muslims more freedom within its borders? If there was, it wasn't by much.
And yet a single set of cartoons in a small Danish newspaper caused the entire Muslim world to rise up and unify behind utter vilification and hate towards the entire nation of Denmark and all of Scandanavia, including serious death threats and actual deaths, that continues to this day.
Now, imagine that the US had adopted the strategy advocated by the authors of this paper. The Muslim logic of Jyllands-Posten is that an entire nation is responsible for the blasphemy of a single act by a private institution. Is it conceivable by anyone, from a typical red-state redneck all the way down to Harvard intellectuals, that the Muslim attitudes towards the US would moderate in the least as long as US newspapers and Hollywood studios and book publishers remain independent? Is it possible that in a nation of 300 million people who treasure freedom that none of them will do something that upsets the Muslim world to the point of riots? Or would the authors also advocate that the US shut down the Washington Times and the New York Post because their existence (like Israel's) could cause Arabs and Muslims to seethe?
The US, as the leader of the free world, stands for everything that Islamists are against, and no amount of support for Arabs (such as billions in aid given every year) will change that fact one bit.
The dhimmified attitude of academia may or may not be related to the funding that it receives from those who advocate terrorism, but it is clear that there is no relationship between the ability to write papers and intelligence. To even consider that the foreign policy of our nation be held hostage to a large group of fundamentally irrational people who hate us is the height of stupidity, notwithstanding that those who espouse such views can also write in multisyllabic words.