Mojang is very explicit.
You may charge for access to your server.
You may charge for banners, colored things, vanity items. You may charge for having bright yellow letters saying "VIP" in front of your name.
You may not charge extra and give different/extra items that help players beat the game and other players to only some players.
You may charge $15 for server access and give EVERYONE the same amount of free diamonds, invisibility potions, and sharpness V swords.
You may NOT charge $5 for 10 diamonds, $3 for 10 invisibility potions, and $1 for a sharpness V sword.
I.e. you are not allowed players to "pay to win" on your server. Apparently they were getting a lot of complaints from customers or parents of customers about servers using this business model. Some have alleged that bukkit members were connected with or running P2W servers so that's why they were so upset.
Reading the bukkit goodbye's, it was probably a lot more complex than that. Some were probably running P2W servers, many were just burned out, some were upset that the original 4 founders of bukkit got jobs but they didn't (and some were apparently more active than some of the 4 founders). At least 6 non founders had made significant contributions to the project.
And a lot took Mojang owning the name and the repository/distribution setup to mean Mojang owned Bukkit.
I think Wes felt bukkit had enough stroke to force Mojang's to give in.
I also think Wes misjudged things, ruined his rep with a lot of people and perhaps with potential employers.