Over at Open Left, and here there has been vigorous criticisms of Obama's campaign, especially in light of his decision to keep McClurkin on-stage. This has led to many doubts about Obama's ability to run a campaign or that he is responsible for running a superficial, personality-driven campaign. The first, and most significant criticism (specifically by Chris Bowers) is a misunderstanding the power of the netroots to shape the primary campaign. The second is a misunderstanding the constraints Obama placed upon himself as he began articulating his campaign. In any event, why Obama is floundering now, for many critics, is due to both outside events and the frames the netroots and the traditional media painted Obama's campaign.
First, 2004 showed the limits of the netroots to elect a presidential candidate (even though I agree that the netroots have matured since then). Unlike congressional races, more attention is paid toward the primary (and general election), by the public and interest groups alike. A reason why Dean was successful was that he was able to gather a lot of attention during the "invisible primary" season, while the other candidates were expecting a different sort of race. The attention on Dean's candidacy captured the focus of the traditional media - thus propelling him into the lead. Kerry and Edwards were slow(er) to receive attention - and slow(er) to respond to the new campaign. In 2007, every Democratic candidate is waging an open primary in the "invisible primary" season. This makes it unlikely that any one candidate (especially a long(er) shot) is going set the terms of the primary season.
Second, the netroots does not have a clear favorite in the Democratic primary. Front-page authors have publicly refrained from endorsing a candidate, and are quick to criticize any campaign, and the "grassroots netroots" are split between Edwards, Obama, and now Dodd (with a vocal, but growing group of Clinton supporters). Also, over the past year, there appears to be a narrowing of what it means to be "progressive" - with the emergence of a litmus test that many diarists subscribe to (most prominently on the issue of residual forces). This makes it easier to find flaws in any of the candidates.
Jumping from the netroots to the campaign, I believe that you do not understand the difficulties Obama faced from the beginning, and the tightrope he needed to walk in order to beat Clinton. What has happened over the year is that Obama's message of transcending politics lost to a practical belief that we (as Democrats) need to win this election. As such, we are drawn to leadership - bold pronouncements denouncing the Republicans (now) - instead of putting faith in a new kind of politics or that a new kind of (progressive) politics is possible.
The second reason why Obama is failing to make this argument was that he was accused from the beginning, by both the traditional media and the netroots, of not putting meat into his stump speeches. People wanted to know his policies from the beginning of his campaign, and he was unfairly compared to Edwards (usually by Edwards supporters) as not having any substance. That frame caught on. In the netroots, people are surprised and react positively to Dodd's statements on the AG, telecom immunity, and other positions of leadership, while Obama usually does not get the same credit when he does take a stand. That being said, Obama has played it cautiously (nearly too cautiously for me), in taking a sharp position on the issues that progressives care about. Another frame that the netroots has bought into is the blurring of Obama and Clinton. Opponents of Obama charged from day one that Obama would compromise on progressive (or Democratic) principles, and would be a repeat of the Bill Clinton DLC years. I think that any neutral analysis of Obama's history and voting record would not bear that out. These two frames have doomed Obama's standing in the netroots.
Additionally, Obama's post-partisan politics is also pragmatic, for the moment. He, nor any other Democrat, benefits from attacking Clinton. Primaries should be ideological battles, not personal ones. In this sense, the issue that would harm Clinton the most would be that she is much more of an elitist (and tied to Washington) than the other Democratic candidates. However, the more she is torn down by the left (on extraneous non-issues), the more likely it is for Democrats to not get excited about the general election. Already, Republicans are running against Clinton as the incumbent, while Democrats (especially with Clinton as the nominee) to ensure that the failures of Bush are on everyone's minds when they vote.