What's the real reason that it's not considered 'canon'?
There were several things that coincided, and most had to do with avoiding expensive red tape (lawyer's bills!) in the easiest way possible: asking that TAS not be referenced.
In early 1989, Paramount renegotiated the contracts for all the tie-in licensees, and Richard Arnold, for the Star Trek Office, specifically asked Pocket Books and DC Comics to stop referencing TAS. (See a brief quote of "the memo" in the lettercol of DC's Star Trek Series II, issue #1.) FASA lost its license altogether.
At around the same time, Filmation had been divided up, wound down and sold off (partly to Hallmark, IIRC), and the screening rights to TAS
and all of the Filmation back catalogue were in a temporary state of flux. Larry Niven was negotiating a "Ringworld" RPG, and his kzinti had been appearing in a semi-licensed RPG, "Star Fleet Battles", against his wishes(?). And DC Fontana and David Gerrold were involved in a lawsuit with Roddenberry over the creation of TNG, so it perhaps makes sense to de-emphasize their involvement with other Treks.
TAS had not been on air in many markets for some years, so it was pointless to hold TNG's screenwriters to being faithful to 22 animated episodes that new and old audiences weren't even able to access.
When Roddenberry passed away in September 1991, the tie-ins started referencing TAS again, beginning with a brief mention of the Phylosians in Jeri Taylor's novelization of "Unification". And Paramount's official Trek website of the time added TAS references and an episode guide.
I hope I got all this correct. A few times people have quibbled over my memories of all the events that were occurring at this time.