The situation seems to have started with tweets about a conversation between some Minecraft server owners and Minecraft developers, where a developer pointed out that charging money for gameplay features is technically not allowed under the game's license agreement. This resulted in many many posts talking about how this was the end of Minecraft servers.
Mojang released a blog post last Thursday on the topic, and another one with an FAQ that further explains the situation today. It clearly lays things out: You cannot charge money for gameplay elements of Minecraft. That may seem obvious, so why was this so upsetting to everyone?
There are a lot of amazing Minecraft servers that do everything from replicate other games to create entire new games. Some servers also run the vanilla game, but for hundreds of people at a time. Most of these servers cover costs with some kind of donation feature, as well as often selling in-game abilities, commonly referred to as "ranks". Ranks can be anything from the ability to kick someone off the server to let you join when it's full to the ability to fly or summon restricted items like TNT.