Looks like CBS is really making mountains out of mole hills with regards to Atrios and his working relationship with Media Matters for America.
If you read 3 posts on his blog you can tell that he's a liberal, so you can assume most people reading his blog are liberal too. I'd bet a good number of those people also read Media Matters, so I doubt that they were upset with Atrios, when they found out that he works for Media Matters.
If anyone has a reason to be upset about all of this, it's Media Matters. Not because of any conflicts of interest, but because they run a really nice information based website.
Atrios, on the other hand, is more into giving his opinion. Which is fine, but it gives the right ammunition when they argue that Media Matters is a partisan attack dog.
...in the end, I can't really get to upset with Atrios being mistreated, 'cause I think he's a dick.
...but that's a whole 'nother matter.