Rapinoe, along with many other athletes, kneeled before the national anthem at the Tokyo Olympic Games in an effort to shed light on issues facing the black community in the US, according to Business Insider.
Some Subway customers are viewing her display as being "un-American," and are vowing to boycott the fast food restaurant chain until advertising featuring Rapinoe is removed.
"As long as you have Megan Rapinoe representing your company, I won't buy another sandwich from your stores," one customer wrote on the Facebook page for a Subway in Bakersfield, California.
Rapinoe was part of a number of celebrity athletes featured in Subway's new adds, including Stephen Curry, Serena Williams, and Tom Brady.
One Subway operator reportedly found a handwritten sign posted to his door, stating: "Boycott Subway until Subway fires the anti-American."
Frustrated with CEO John Chidsey over a failed promotion attempt for their new menu, franchisees complained in a private forum about the misuse of advertising funds.
"By knowingly hiring a flashpoint personality to represent the brand with our money, the franchisor has failed," one operator wrote in the private franchisee forum seen by Insider.
Subway advertising is currently funded by a 4.5 percent fee as part of operators’ overall royalty fees, but the franchisees, however, have no say in how the ad money is spent.
Franchisee Mario Denoto told Business Insider that celebrity spokespersons can be "polarizing" for customers who "can go either way with them."
"Please end Megan's commercials," Denoto said he told corporate in an email sent Tuesday.
The North American Association of Subway Franchisees, Subway's main franchisee group, communicated backlash from received from customers over Rapinoe's featured advertising, according to the private forum.
The "super-star athletes are a natural fit for the Eat Fresh Refresh campaign" and are part of the chain's effort to drive visits to stores owned by more than 10,000 US franchisees, a Subway spokesperson told Insider in a statement.