"Whether it is challenging governments, educating the public, or training journalists, we have a long history of helping bring online freedom to more people around the world," stated the text an Apple app reviewer had an issue with.
The reviewer suggested the text be modified to not "encourage users to bypass geo-restrictions or content limitations".
Yen used the rejection to claim Apple was stymieing rights in Myanmar, which is in the midst of a brutal crackdown following a coup last month. The founder said the company had used the description for months already.
"Actions have consequences, and Apple's actions are actively hampering the defense of human rights in Myanmar at a time when hundreds of people are dying," Yen said.
It's a far cry from its famous 1997 ad when the company said the following words over the top of a montage of government resisters: "Here's to the crazy ones. The misfits. The rebels. The troublemakers. The round pegs in the square holes. The ones who see things differently. They're not fond of rules. And they have no respect for the status quo."
Last week, Wired reported that Apple had agreed to begin showing Russian users a phone setup screen where they could install a set of Moscow-approved apps.
"Apple's priority is to preserve access to markets and maintain its profits, so it almost never challenges the policies of dictators or authoritarian regimes," Yen said.
"By giving in to tyrants, Apple is ignoring internationally recognised human rights and preventing organisations such as Proton from defending those in need. What is also troubling is that Apple requested the removal of this language in ALL countries where our app is available.
"By doing so, Apple is helping spread authoritarian laws globally, even in countries where freedom of speech is protected."
In response Apple said all of Proton's apps remained available in Myanmar.
"We approved the most recent version of ProtonVPN on March 19. Following this approval, Proton chose to time the release of their update, making it available on March 21st, while subsequently publishing their blog post on March 23rd," the company said.
Apple said in a submission to the Australian Competition and Consumer Commission recently that it was surprised developers took issue with its app review process.
"The main purpose of the App Review process is to protect consumers from fraudulent, nonfunctioning, malicious, or scam apps," Apple said.
"Central to the App Review process is the protection of our consumers' privacy and security."
Updated at 12:19pm AEDT, 25 March 2021: Added Apple comment.