Shoot, I thought they were canon too. I thought that was the point of the new comics being done by JJ's people.
The point was to keep them as consistent with canon as they could, which isn't the same thing as actually being part of the canon. But I think Bad Robot underestimated how difficult it would be to keep the tie-ins consistent with an ongoing canon.
Well so far they've done a decent job of it seeing as the only major contradictions are a few lines of dialogue.
Thats pretty much the level of effort into continuity most long running tv shows manage. Not to mention film series, book series, and ect.