Due to Apple's size, the tech giant has unfairly become "a punching bag" over the latest questions about its older iPhones, CNBC's Jim Cramer said Wednesday.

Republican Sen. John Thune sent a letter to Apple CEO Tim Cook, Reuters reported, asking questions about its disclosure that it slowed older iPhones with flagging batteries.

Apple announced last week customers can now replace batteries on the iPhone 6 or later models for $29. It came after the revelation that its software slows down older phones to protect battery stability.

"Apple's become a target," said Cramer, whose charitable trust owns shares of Apple. "It's so big, they've really become a punching bag. And I find it interesting because there are a lot of companies that do a lot of things that are not necessarily pro-consumer."

"Apple's become so big it's become, 'Wow, let's attack Apple,'" Cramer said on CNBC's "Squawk on the Street."

Cramer commented earlier this month on the news about older iPhones, saying it wasn't a big deal and investors shouldn't sell their stock.

The company and others are so big they're like "countries" and easy political targets, Cramer said Wednesday.

"They've become countries to some degree," said Cramer, the host of CNBC's "Mad Money." "When you see Apple and everyone has one, you're tempted to say, 'Wait a second. There is something that is wrong with this device that everyone uses?'"