Consider that Mr Silver has been given awards and accolades most journalists would kill for: Time's list of 100 most influential people in the world, best political blog Webby award, Rolling Stone's 100 agents of change, the editor in chief of Politico listed him as "one of the most powerful people on earth", he's given a prestigious lecture at Columbia Journalism School, etc. He's received accolades, even from traditional journalism sources, that most journalists, even at the NYTimes, would never dream of. Speaking of which, the Public Editor of the Times wrote "he’s probably (and please know that I use the p-word loosely) its most high-profile writer at this particular moment."
All this for someone who has never worked a proper newsroom since college, never had a television show, cable or otherwise, and just started a blog four years ago because he was (supposedly) annoyed at laws that threatened his livelihood - online poker.
So imagine seeing someone like this receiving all the awards you've coveted since you started journalism in earnest. While the recoil against Mr Silver might be clothed in intellectual differences for some, the reason they care probably has more to do with seeing someone who differs from their traditional approach getting so much recognition.
Finally, I'd note that there are many traditional journalists who support Mr Silver's approach - his awards from traditional journalist organizations speak to this. Rather, it's a very specific group that seems to feel threatened.