The Muslim Brotherhood is the leading opposition group in Egypt's political system. Though it officially is outlawed in the country, its members -- who run as independents -- hold 88 seats in Egypt's parliament.
Ibrahim Al-Houdaiby, 25, a Cairo-based activist who works for the Brotherhood's Web site, told FOXNews.com after Obama's speech that it was a "step in the right direction," but he was disappointed the U.S. president seemed to give a pass to leaders like Egypt's own Hosni Mubarak.
"He didn't mention any authoritarian regimes in the region," said Al-Houdaiby, who includes Egypt's regime in that category.
Al-Houdaiby did not attend the speech, though a group of Muslim Brotherhood lawmakers did.
"There are tens of thousands of political prisoners who have nothing to do with violence and have nothing to do with terrorists" in Egypt and across the Middle East, he said.
Though Egypt holds elections, Mubarak has ruled as president since 1981 and frequently is accused of suppressing political opposition. Human Rights Watch wrote in a column ahead of Obama's visit accusing Mubarak's security forces of having "violently suppressed strikes and peaceful demonstrations."
Mubarak's government has arrested and imprisoned members of the Muslim Brotherhood, accusing it of aiding violent Islamic organizations.
Al-Houdaiby said Obama did not give enough attention Thursday to the promotion of democracy and human rights in the region.
"If you're speaking for universal values, then human rights are universal values," he said.
He also said Obama's speech contained few specifics about a two-state solution between the Israelis and the Palestinians.
Even so, he said, Obama's overall theme about "rebuilding bridges" was a positive step. He also praised Obama's approach to women's rights: The president stressed that it a woman's may choose to live in a "traditional" way.
The Muslim Brotherhood's invitation to the speech, though, drew some criticism from the U.S., since the fundamentalist group seeks the establishment of an Islamic state and has ties to the militant Hamas.
Scott Wheeler, director of the National Republican Trust, a conservative political action group, slammed the administration for apparently allowing the Muslim Brotherhood into the event.
In a written statement, he charged that the group is linked to "international terrorists attacks, advocates suicide bombings, and the very founders of Hamas."
"The American people did not vote for President Barack Hussein Obama to make peace with Muslim terrorists," he said in the statement.
Al-Houdaiby, though, said such criticism is unfair, as the Brotherhood claims to have renounced violence.
"The Brotherhood is a very broad and huge school of Islamism," he said, insisting that violence for political means is not part of their apparatus. "You can't make judgment on a group as wide and diverse as the Brotherhood."
Despite some reports suggesting the Obama administration arranged the Brotherhood invitations, officials said invitations were only sent out by Cairo University and Al-Azhar University.
FOXNews.com's Judson Berger contributed to this report.