A South Carolina restaurant owner is planning his own counterprotest against NFL players who are kneeling during the national anthem, and it could have major consequences for his business.

David McCraw, owner of the Palmetto Restaurant and Ale House in Greenville, said last Sunday that he won't show any NFL games until all professional football players stand during "The Star-Spangled Banner."

While sales at McCraw's restaurant could get a slight jolt from like-minded customers in the near term, ultimately, the decision could backfire for the business.

"We advise clients away from taking these politically charged positions," Aaron Allen, founder and CEO of global restaurant consulting firm Aaron Allen and Associates, told CNBC.

While supporters may flock to an establishment after it takes a position on a hotly debated topic, the lift in sales won't be long-lasting, he said.

"If they were going for those sports and the sports are gone, they are, too," Allen said.

Allen estimates that events such as an NFL game, the Olympics or a boxing match can boost revenue by 30 percent or more on the day of the event. However, for Jason Emmett, president of Duffy's Sports Grill, that growth is much higher.

Emmett told CNBC that sales on a football Sunday are 66 percent higher than that of regular Sundays throughout the year.

At many restaurants and bars, NFL games are a huge draw for customers, especially those who are fans of teams that are not featured on their local cable network. Customers will spend upwards of three hours in these locations, purchasing food and drinks while they watch the game.

Tabs on average range from $20 to $40 for beer alone, according to one New Jersey bartender, who wished to remain anonymous.

"NFL football is an institution here at McFadden's," said Kristi Paris, chief marketing officer for East Coast Saloons, which owns McFadden's, a prominent Buffalo Bills bar in Manhattan. "We have a crowd of 300 Buffalo Bills fans who come to support their team and fellow fans for every game at McFadden's. They comprise a huge chunk of our business during football season."

For McCraw, this decision could have a ripple effect that lasts much longer than just this NFL season. Customers who have sought out other venues to watch the game may not return even if Palmetto does begin to show professional football games again.

"Once you've changed [the customer's] behavior or habit, it's hard to change it back," Allen said.

Representatives of Palmetto Restaurant and Ale House did not immediately respond to CNBC's request for comment.