The fight between the European Commission and Apple reminds Roger McNamee, co-founder of Elevation Partners, of the U.K. vote to leave the European Union.
"I look at this and I go, 'This is a different environment than the one we've been in.' Brexit is part of the same trend," McNamee said Tuesday in an interview on CNBC's "Squawk Alley." "People are less willing to subsidize those who can contribute to their growth and much more focused on maximizing the share of the pie they get from taxes."
Earlier Tuesday, the European Commission ordered Ireland to recover up to $14.5 billion plus interest in back taxes from Cupertino, California-based Apple. Both the iPhone maker and Ireland are planning on appealing the ruling.
While the current global tax infrastructure is "crazy, ... it exists because we've had a political culture that favored growth and was willing to give tax benefits in order to cause that," McNamee said.
"This is a political problem. It's not going to resolve itself in the stock market. The stock market is just going to react to whatever the outcome is."
The market seems to believe that subsequent negotiations will take a long time to play out in court, according to Toni Sacconaghi, senior internet analyst at Bernstein. He pointed to the relatively small move in Apple shares on Tuesday, which were down a little more than 1 percent.
Although the European Commission set the back taxes Apple owes to Ireland at $14.5 billion, Sacconaghi said it's unclear what the company would actually pay, if anything. He said there's also "uncertainty about ongoing tax legislation that might make Apple's future tax rate higher going forward."
Following the commission's ruling, Apple CEO Tim Cook fired back and said that "in Ireland and in every country where we operate, [Apple] follows the law and we pay all the taxes we owe."
"I think historically, Apple has been unwilling to negotiate on many different fronts, whether it with be suppliers, whether it be around the privacy issue that we experienced earlier this year and in the U.S. Apple is pretty steadfast in its principles," Sacconaghi said on "Squawk Alley."