Just my two cents here...
It's Matt's job to cover the system, not support the system 100%. It's not his job to be a Nintendo fan. Just because he isn't sugar coating problems, issues, etc. does not mean he's not a Nintendo fan. If things are going rough, why not say so? He's supposed to be an editor at a video game site, not a fanboy. I enjoy and respect the fact that he's not afraid to say "hey, Nintendo is screwing up on this one" or "for this and this reason, an XBOX might be a better choice". He wasn't "bashing" Nintendo - but the company faltered with the Cube, and he was not afraid to bring the faults to light and discuss them. I am glad that I didn't have to visit the IGN Cube site every day only to read nothing but shining praise for Nintendo, when clearly they had made mistakes. Being a video game company, they know they're under the spotlight (especially with gaming media), which makes the mistakes all the less immune to extreme criticism. I do not want to go to a video game website and read a bunch of stories that are written for the purpose of "supporting" the system or making it look good - I want to read about the system, what's going good and what's going bad. Matt isn't jumping on the "I love Nintendo" bandwagon - he's been there all along. Just because there were problems to point out on the Cube does not mean that he abandoned the company. It means that there were problems to point out.
I don't think he lacked the spine to defend Nintendo - he gave credit where credit was due, and he criticized where that was due as well. And of course the media is going to have an effect on the image, etc. of a console - however, in my opinion they bring out the problems with the console/company, not create new ones. If Matt's influence can sway buyers, that's all the more reason to express the negatives as well as the positives. If not, then to me it's just like reviewing a terrible game, and saying "the disc comes in a case, and the game runs, plus it's for GameCube so give it a shot!". Pointing out the negatives is just as important as pointing out the positives.
Case in point: it's my opinion that the media magnifies the moves that the company makes, and the image that the company creates (whether that image was created on purpose or not). Therefore, whatever is magnified, started with the company. I like being able to go to IGN (Cube and Wii, anyway), and hear what is going wrong AND what is going right. Feed me some negativity - if it's not a lie, then that's what I came there to read in the first place. And for the record, Matt did acknowledge with the Wii that Nintendo was on to something, but was cautiously optimistic about it.