The nexus of Pro-Darwin lobby (teachers, pundits, parents, etc.) and biology practitioners worried about the political status of evolutionary science often work together to make this worse, and not simply by hateful negative attacks on their opposition or by failure to dumb it down sufficiently. (A point not made well by Flock of Dodos.)
As with many evolution-related issues, there is at best a double-message going out there. One is that neo-Darwinism has never had any serious deficiencies and therefore never needed any balance or controversy taught, which has been a useful tactic of the NCSE for years. (Whether this is a vestigial behavior--the "pro-science" lobby has evolved much more slowly than the "anti-science" crowd--or whether this is the inherent defensiveness of a dominant paradigm is a story for another time.) The other message is that there is vigorous, healthy debate over what the processes and mechanisms of evolution are, but that since almost all of these are believers in both methodological naturalism and the power of known forces to explain everything, the commonly taught evolutionary hypotheses are unassailable facts (or should be taught as such at any rate).
The former message has certainly hurt Darwinism. How much criticism has there really been against Richard Dawkins by the "pro-science" coalition for his extreme neo-Darwinistic reductionism? Randy Olson's poker-players don't seem bothered by him. The closest that Olson gets at all to noting any challenge to neo-Darwinism (or that there is any diversity in the academic ecosystem) is lumping "process structuralism" in with ID at some point (the "teach the controversy" segment, I think). The fact that Olson can implicitly charge ID as a God-Did-It approach (as his editing choices convey) but not recognize the extent to which much of evolutionary literature has boiled down to Selection-Did-It or Evolution-Did-It says much. In fact, the ideas about how it happened and the mechanisms involved are so complicated at this point, that overconfidence concerning natural selection through most of the 20th century (and continuing now) seems both naive and quaint. I was taught in college that microevolution = macroevolution, essentially, as a fact. As Stuart Newman has pointed out, this overconfidence, while achieving political mileage in jurisprudence, has hurt public perception of evolutionary teaching in general.
Meanwhile Michael Ruse has attacked creationism (no doubt including ID in it) of being more selection-obsessed than the evolution crowd, without (until perhaps lately) giving any credit to this sociological effect. If people tend to conflate anti-Darwinism with anti-evolution, maybe it's because too often the "pro-science" crusaders have conflated Darwinism with evolution.
The second message potentially hurts the general prospect of evolution partly because of this (wait, what do you mean it isn't as simple as natural selection and microevolution?), but also because Selection-Did-It is more obviously replaced by Evolution-Did-It. Evolution has become the Dark Energy of the 21st century. No one agrees what Dark Energy is or how it figures into physics, but Something is causing the galaxies to diverge over time; new species with novel structure and organs have appeared over time and therefore Evolution is the name given to that Power at work. The entire scientific community starts to a resemble a jury that have very conflicting ideas about how the defendant committed the crime and where he committed it, based on contradictory evidences and contradictory interpretations, but are (almost) unanimous in their belief that he is most definitely guilty based on the evidence. (Half the jury are okay his religion, half are okay with his race, and only a few don't like his face, so you can't say they are unanimously prejudiced.)
But if we give the name "Evolution" to the basic pattern being investigated--the changes in biological diversity over geologic time on Earth, the explananda rather than the explanans--neither Intelligent Design in general nor Discovery Institute in particular are any opposition to this. The fact that you can be a creationist within the ID framework, as you can be an evolutionist like Michael Behe, or anything in between, is part of the guilt-by-association tactics by "pro-science" Big Darwin. What the "pro-science" lobby find so threatening about the "Big Tent" of ID is that (a) that it is mostly consonant with theism (i.e. "makes it possible to be an intellectually fulfilled theist") rather than dissonant, and (b) the usual tactics against Young Earth Creationism do not begin to address it.
(Again, two messages: (1) Creationists are not to be trusted because they are evolution-denying hayseeds. (2) ID theorists like Michael Behe who largely embrace evolution are still creationists because they don't rule out theories consonant with "supernatural causation." Collectively, these messages amount to double-speak.)Certainly, you can be a skeptic of neo-Darwinism without doubting Big Evolution. What Suzan Mazur's work has achieved, perhaps more than anything else, is documenting the stifling effect the neo-Darwinian Synthesis has had on biologists and selection skeptics. But calling evolution skeptics "evolution deniers" (a trope that analogizes with Holocaust denial) is partly ugly political tactic and partly "physics envy" (the idea that biology vies with physics for ontological validity, e.g. in elevating the theoretical status of evolution to that of gravity). Many ID theoreticians believe in some version of selection-oriented evolution and common descent, many are skeptics of one or more accepted evolutionary hypotheses, and some do think the whole evolutionary narrative is a mostly unproductive concept.
The crumbling of the neo-Darwinist edifice has hurt Evolution in more than just a PR sense. If science, as the ACLU has asserted through Judge Jones, is what scientists do, then neo-Darwinism is the strongest, most worked out, and most explanatory theoretical framework for evolution. If it is really as weak as it appears to be, it calls for some serious skepticism of the explanans of evolutionary science, if not the explananda.
Perhaps the biggest failing of Randy Olson's Flock is the attempt to only cast Intelligent Design as a sociological phenomenon (driven by philosophical motives) and does not really get close to doing the same with his own camp, despite his belief in his own objectivity. He shows some of this at work, but doesn't make it part of his documentary's explanation. The explanation he gives concerning them is that they are so erudite (he helps make this point by displaying definitions for the big words they use) that they make poor evangelists for his gospel of truth.