Axanar violated the principle that while CBS/Paramount does not like fan fiction, they tolerated it as longs it didn't take money out of their coffers. Axanar by it's very existence took money out of existing official Trek products.
Look I work for an organization that is kinda
litigiousness about our IP (We own the rights to 5 interlocking rings, and if any one try to make a logo with 5 interlocking rings
WE WILL SUE YOU FOR IT)
Axanar violates more than just The broad Star Trek IP. It Violates ship styles, configurations and other things. Not to mention CBS/Paramount's multiple licensing agreements INCLUDING Star Trek Online. Hell I'm surprised CBS waited this long. Ultimately the fan productions that followed the rules are the one that's hurt not by CBS or Paramount but by Axanar.