They differ with Al-Qaeda on the means, not on the goals.
Here is a pdf of the full report. See especially pages 27 through 30: “Islamist Groups and Shari’a.” On page 27, the report says: “The Islamist goal of giving Shari’a a larger role in Islamic society is viewed positively.”
And on page 29: “In Egypt 81 percent said they agreed with the al Qaeda goal of “requir[ing] a strict application of Shari’a law in every Islamic country” (65% strongly); only 12 percent disagreed. Pakistanis were similar with 76 percent agreeing with this goal (52% strongly); 5 percent disagreed. Indonesians, however, agreed by only a narrow plurality: 49 percent supported the goal (just 14% strongly), while 42 percent disagreed. In Morocco in late 2006, 76 percent agreed.”
“Muslim Publics Oppose Al Qaeda’s Terrorism, But Agree With Its Goal of Driving U.S. Forces Out” a press release:
COLLEGE PARK, Md., Feb. 25 /PRNewswire-USNewswire/ — A study of public opinion in predominantly Muslim countries reveals that very large majorities continue to renounce the use of attacks on civilians as a means of pursuing political goals. People in majority-Muslim countries express mixed feelings about al Qaeda and other Islamist groups that use violence, however, perhaps due to a combination of support for al Qaeda’s goals and disapproval of its terrorist methods.
Large majorities support allowing Islamist groups to organize parties and participate in democratic elections. In some majority-Muslim countries, Islamist groups, such as the Muslim Brotherhood, are forbidden from participating in elections….
The survey is part of an ongoing study of Egypt, Pakistan, and Indonesia, with additional polling in Turkey, Jordan, the Palestinian territories, Azerbaijan, and Nigeria. It was conducted July through September, 2008 by WorldPublicOpinion.org with support from the START Consortium at the University of Maryland. Margins of error range from +/- 3 to 4 percent.
In nearly all nations polled more than seven in 10 say they disapprove of attacks on American civilians. “Bombings and assassinations that are carried out to achieve political or religious goals” are rejected as “not justified at all” by large majorities ranging from 67 to 89 percent. There is a growing belief that attacks on civilians are ineffective, with approximately half now saying that such attacks are hardly ever effective….
Views of al Qaeda are complex. Majorities agree with nearly all of al Qaeda’s goals to change U.S. behavior in the Muslim world, to promote Islamist governance, and to preserve and affirm Islamic identity. However only minorities say they approve of al Qaeda’s attacks on Americans….