According to Paula Block of Viacom Consumer Products: "Another thing that makes canon a little confusing. Gene R. himself had a habit of decanonizing things. He didn't like the way the animated series turned out, so he proclaimed that it was NOT CANON. He also didn't like a lot of the movies. So he didn't much consider them canon either. And--okay, I'm really going to scare you with this one--after he got TNG going, he...well...he sort of decided that some of the Original Series wasn't canon either. I had a discussion with him once, where I cited a couple things that were very clearly canon in the Original Series, and he told me he didn't think that way anymore, and that he now thought of TNG as canon wherever there was conflict between the two. He admitted it was revisionist thinking, but so be it."
Here's the link to the entire report. It was written before ST09 but includes ENT.
Thanks for finding that article. It's a good reminder that canon isn't some gospel carved in stone, it's just the current opinion of the current creators. And creators change their minds all the time. That's key to the creative process itself -- we write stories by testing out possibilities, by revising and refining them, by discarding and replacing the ones that don't work. And over time, we inevitably come to regret some of our earlier decisions and want to paper over our mistakes.
So canon really doesn't mean all that much. Dwelling too much on what falls under that label just gets in the way of enjoying the stories being told.