One wonders what one is supposed to be able to infer from the mere existence of an Independent Lens documentary. Perhaps you could tell us about some of the other Independent Lens documentaries that you've seen, and relate the motivations for their production, so that we can see how this inference is supposed to work? Is it your contention that any subject of an Independent Lens documentary is, by default, a politically controversial phenomenon?
The best explanation for both of those things is exactly that The 99, and the narrative about American TV execs resisting it for ideological reasons, makes great fodder for the Independent Lens audience, and plays into the PR narrative that its producers have ridden to success so far.
It's worth keeping in mind that the entire motivation for turning The 99 into an animated series and pitching it to US television, is exactly that it does not sell enough to turn a profit in any of the Arabic-language markets it already appears in, despite warm reception from the media there and open backing of local politicians. Remove that agenda from the decision-making - leave it up to a bunch of executives who only care about profit - and the lack of airtime doesn't seem to demand anything beyond simple profit motive in the way of explanation. Of course, the producers of such could never simply admit that - and certainly, not in the documentary about them which is their big chance to pitch their product to a wider audience - so, unsurprisingly, we get a self-serving narrative about how their great, profitable product is being censored due to bigotry.
But, answer me this: have you read or watched any episodes of The 99? Did you pay to do so? Would you pay to read/view more of such? Do you have any reason to assert that anyone stands to make any money by distributing such? Or is the whole production simply a political football?