The headline from that link:

"to ferment is to cause a chemical change to food or drink, like turning grapes into wine, but to foment is to stir up trouble, like turning a group of people into an angry mob."

Fermenting is a fancy word for rotting. Fomenting is arousing or inciting. Neither have necessarily positive or negative connotations. One could ferment a tasty ale or a noxious concoction. One could foment civil disobedience or civil war.