It can be seen in the controversy surrounding the construction of an Islamic community center in New York City. It resonated around the world when a Florida pastor threatened to burn a copy of the Quran. And it goes on today as politicians propose legislation that would ban mosques from communities across the country.
The perception of Muslim Americans took a turn for the worse in the decade since the attacks on Sept. 11, 2001.
"They think Islam is not a religion, it's terroristic, they will bring jihad into America," said Rudy Zarzar, professor of political science. "They think the Muslims living in this country are like fifth colonists, they want to enact Shariah law. None of this has legitimacy or truth but people believe it and that's what's so sad about this whole thing."
But Americans not only misunderstand Muslims. It also is the other way around. Middle Eastern countries often viewed the war on terror as a war on Muslims.
"When we declared war on these countries, it's funny that all of them are Muslims," Zarzar said. "When you repeat it, that's the perception. I'm not saying that's the way it should be, but sometimes people's perceptions are more important than reality. That's the way they see reality, like it or not."
When the United States pursues foreign policies that are viewed as anti-Muslim, others take note of it, Zarzar said. While bin Laden's methods were never popular with the majority of Muslims, his message did resonate.
"The message that the U.S. is basically anti-Muslim, fights only Muslims, wants to destroy Islam resonates with them because they see cases where (the U.S.) has done just that," he said. "It doesn't mean they agree with terrorism. They think it's doing more harm to Muslims than anything."
The majority of Muslims did not approve of the radicalism of bin Laden and al-Qaida and did not support his idea of "Holy War." The methods of terrorism targeted not only American citizens, but those within bin Laden's own faith.
"Osama bin Laden wasn't only attacking infidels, but also attacking Muslim leaders he thought weren't Muslim enough," Zarzar said. "In the West, there is an unfortunate tendency to lump all Muslims into one package."
Misconceptions such as this often lead to a fear of the religion.
"Unfortunately, you say 'Muslim' and you scare the hell out of people," Zarzar said. "It's called Islamophobia."
The perception of Islam is that it is a warlike religion and sexist, according to Zarzar.
"There is also some truth in myths, but when we say them and don't say, 'yes, this is true, but. . .' then you generate lies and every Muslim becomes a bad guy," he said.
Sophomore Nada Azem, originally from Syria, said she has found herself wrapped up in the unfounded conceptions put forth by Americans.
While visiting ground zero in New York City this summer, she at first felt embarrassed when her mother, who wears a traditional Muslim headscarf, began asking about the former location of the World Trade Center.
"I told her, 'no you're covered, you can't ask,'" Azem said. "I tried to act like I didn't know her."
Before long, they located the site and Azem's mother had broken down into tears. Surprisingly to Nada, there was minimal reaction from the New Yorkers strolling past.
"After I left, I realized I'd been in America for a year and I'd already had the reaction that (Muslims) aren't supposed to do that," Azem said. "All of a sudden, I had fallen into the idea that Muslims aren't supposed to show sympathy for what happened."
Sept. 11 did create sympathy toward the United States among Middle Easterners, especially for the innocent victims, according to Zarzar. This good will was hurt when the United States entered Iraq under the banner of fighting terrorism.
"Given that, whatever good will we received, we lost it because of intervention in the (Middle East)," he said. "Again, we see how the U.S. seems incapable of creating bridges to the Middle East because of policies."
He also cited the United States' "one-sided" support of Israel and alliances with dictators as barriers to peace.
"We are traditionally allies with dictators because we can control them, they served our interests," he said. "If you're Middle Eastern, you would feel resentment and say the U.S. talks about democracy but when it comes to it, we play into the hands of terrorists."