Students were asked to trace Arabic calligraphy in an exercise some parents said amounted to indoctrination.
Officials said the schools were closed out of an "abundance of caution" and there were no specific safety threats.
School administrators say a different lesson will be used in the future.
One week ago, students at Riverheads High School were studying the Middle East and were asked to trace a piece of Arabic calligraphy that translated to: "There is no God but Allah and Muhammad is the messenger of Allah".
Some pupils refused the assignment and parents accused the teacher of indoctrination.
Officials with the Augusta County school district were quick to point out that the study of a region's religion and language are included in geography lessons.
However, anger built up and by Wednesday complaints had become so numerous that the school's doors were locked and monitored.
By Friday, the messages - described as profane and hateful - had increased and the decision was made to close the schools.
Officials said that no specific threats were received, but law enforcement officials and the school district board recommended the closure because they were being cautious.
The lesson was intended to illustrate the complexity of the Arabic language, they said, and not meant to promote any religious system.
But future classes will use a different, non-religious example of Arabic.
The decision to close the schools has drawn criticism as well.
"It looks like fear wins again," a resident told the News Virginian newspaper.
On the paper's Facebook account, locals have been debating the closure with one man saying, "our patriot forefathers are rolling in their graves," and another rhetorically posting, "how do these terrified people leave their houses every day?"

Phoenix, 37, told Interview Magazine: "I don't want to be a part of it. I don't believe in it."
The actor has been tipped for awards success The Master, in which he plays a war veteran.
He was nominated for an Oscar for his role as music legend Johnny Cash in Walk The Line in 2005.
Phoenix said he was dreading the upcoming Hollywood awards season which culminates with the Oscars in February 2013.
"It's a carrot, but it's the worst-tasting carrot I've ever tasted in my whole life. I don't want this carrot," he said.
"It's totally subjective. Pitting people against each other....It's the stupidest thing in the whole world."
Phoenix described the period when Walk The Line was up for multiple awards seven years ago as "one of the most uncomfortable periods of my life."
"I never want to have that experience again," he revealed in the interview.
"I don't know how to explain it - and it's not like I'm in this place where I think I'm just above it - but I just don't ever want to get comfortable with that part of things."
The Master, which also stars Philip Seymour Hoffman, is Phoenix's first feature film since I'm Still Here, Casey Affleck's spoof 2010 documentary which chronicled Phoenix's supposed retirement from acting to launch a career as a rapper.
Phoenix called that experience "unbelievably liberating" and said it was hard subsequently to find projects that interested and excited him.
"I mean, everything that they teach you when you're a kid about acting is completely...wrong. They tell you to memorise your lines, follow your light, and hit your marks. Those are the three things that you shouldn't do.
"You should not learn your lines, you should not hit your mark, and you should never follow your light. Find your light - that's my opinion," he said.

The US economy added 215,000 jobs in July, while the unemployment rate held at a seven-year-low of 5.3%.
The Dow Jones closed down 46.37 points at 17,373.38, while the S&P 500 dropped 5.99 points to 2,077.57.
The tech-focused Nasdaq index fell 12.90 points to 5,043.54.
Although the number of jobs added in July was slightly below expectations, the figures for May and June were revised upwards by 14,000.
Among individual stocks, Groupon fell 5.34% after the daily deals website reported disappointing revenue growth.
Second quarter revenues rose 3.1% to $738.4m, which was below expectations. The firm also said revenues for the current quarter were set to fall to $700m-$750m, from $757.1m a year earlier.
A school district in the US state of Virginia has closed all schools on Friday after a geography lesson that included Islam sparked vociferous complaints from around the country.
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Joaquin Phoenix has said he wants no part in the movie industry awards season, calling the awards "stupid" and "subjective".
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(Close): US stocks fell and the dollar fell against the yen and euro, after the latest jobs figures were seen as leaving the door open to a rate rise in September.