"We are disappointed that Mr. Ailes directed his apology only to the ADL, and amazed that his statement substituted a new insult to replace his original scurrilous remark," read a statement from NPR. "This ongoing name-calling is offensive to NPR, its member stations and the 27 million listeners who rely on us."
At a time when talk radio is on the rise and pundits on both sides of the political aisle are taking over television, the kind of rhetoric being spewed by Ailes doesn't come as a surprise, experts say.
"All of this is part of the larger polarity in news media and in American political life," said Sterling. "The middle is disappearing. This is an example of that."
Some commentators, however, say the right is waging an unfair fight and that if the tables were turned, similar rhetoric from the left would be lambasted by conservatives.
"What would have happened had an NPR host referred to Fox News as the 'Nazi network'?" questioned political columnist David Corn in Politics Daily. "Bill O'Reilly and Sean Hannity would have howled. Conservatives from coast to coast would have called for that person to be tossed off the air -- before being drawn and quartered. House GOPers would have announced hearings and try again to defund NPR. And Sarah Palin would have tweeted."
NPR became the subject of Republican backlash when it fired news analyst Juan Williams in October, after the conservative commentator said he gets "worried" and "nervous" seeing "people who are in Muslim garb" on airplanes.
NPR chief executive Vivian Schiller explained that Williams crossed the line several times in the last couple of years and that "this isn't a case of one strike and you're out." But she also admitted that the firing could've been handled in a much better fashion.
"The way they handled the thing -- it hurts. It brings out the crazies," Sterling said. "It brings out the hardliners on both sides really but certainly the hardliners who think tax money has no business supporting this biased business."
Only about two percent of NPR's funding comes from federally funded organizations. Forty percent of the revenue is generated through station programming fees while 26 percent comes from sponsorships.
NPR stations, however, rely more on federal and state grants. While the bulk -- 32 percent -- of funding comes from individuals and 21 percent from businesses, CPB funding makes up 10 percent of funding and federal, state and local government funding constitutes about 6 percent of a station's revenue source.
NPR on Thursday assailed Republican lawmakers attempts to cut funding, citing it as "an unwarranted attempt to interject federal authority into local station program decision-making."
With Republicans taking over the majority in the next House of Representatives, the debate is likely to continue brewing. But even if the GOP proposal passes under a Republican-controlled House, it's unlikely to pass in the Democratic-controlled Senate.