Not sure what news programs you are watching, but I've seen those stories all over, particularly the first two. There are tons of articles blasting the 49ers for their handling of the Smith situation. If it was a Phins player, people would be whining about how the media has an "agenda" against the team (I'm sure some 49er fans are).
But I guess that doesn't fit the "everyone is against us" thing. What's funny is that the article in the OP is a Florio article, which is strange because I thought he only went after the Phins...
Yes, it was covered in quite a few places, but nowhere with the same ferocity, one huge example, I remember for months on ESPN national radio, every day the bullygate story was being talked about, in one way or the other, while Ray Rice knocking out his girlfriend slowly got less and less reporting.....I guess hurting a 300+ pound Linemen's feelings is more severe then beating up a women to the point of knocking her out cold.
I remember on just the Mike and Mike show alone, each day seemed like it was more " The new angle on bullygate for today show."