The title is quite deceptive. Reading the Wired article, Apple seems to be pursuing a trademark in Switzerland on a depiction of an apple (without bite mark, and in black-and-white). The Swiss authorities granted this but only on limited product categories. Apple filed an appeal about this, which is ongoing.

Now, the Fruit Union is fear-mongering / spreading the message that, if this appeal is granted, they would be forced to change their logo. However, it seems there is no direct threat from Apple to the Fruit Union. Also, it seems unlikely Apple's appeal will actually be granted, as there is "a legal principle that declares generic pictures of common goods to be in the public domain".