Most fans of any given show are actually not invested enough to talk about it online. Places like TrekBBS and Gateworld don't represent the mainstream fans, but rather the hardcore fans. Gateworld has about 42,000 members. SG-1 got canceled having somewhere between 1-2 million weekly viewers, right? The entire Syfy forum has 146,067 members, and presumably millions of people are watching their shows. TrekBBS has 21,209 members, while at its peak TNG was pulling over 10 million viewers a week.
You see what I mean? Online fandom is a tiny fraction of a fraction of the people who actually watch (or ever watched) a show. In other words, their opinions don't really matter when it comes to making business decisions.
SGU didn't fail because people here and over at Gateworld didn't like it. It failed because a couple million people gave it an honest chance and they didn't like it. They were bored, turned off, whatever.
Tie-in books generally don't sell that well to begin with, either. Saying the Stargate books don't sell well because they're not canon assumes the general book-buying public cares about such things. They don't. They care primarily about whether the book has good reviews and good word-of-mouth, or they just buy it on impulse. Canonicity may be of concern to hardcore fans, but not to anyone else.