The main issue with groups pushing single boogiemen is that life isn't that neat: there are, as alluded to in other places, multiple people (mostly billionaires these days, but not always) with major influence pushing multiple opinions. I am also not surprised that life behind the scenes at one of these advocacy groups is as Dilbertesque as any corporate environment tends to be.
I think the main issue here is that, with decisions like Citizen United in particular, political power does seem to have shifted towards those who can spend the most money even more than usual. Often, their priorities are out of whack with what the priorities of the common citizen are. I do not get the impression, for instance, that tax cuts aimed largely at corporations and high earners were the top priority of most who voted in last year's election (certainly the polling on the tax cut seems to reflect that). Yet this appears to be the single issue that the national GOP unifies itself on. Go figure.
Paradoxically, I think the very messiness that you are talking about might actually contribute to this particular issue. Instinctively, the Koch corporate interests shouldn't care about muni broadband much. Koch is largely resource extraction, meaning a lot of operation in rural areas. Given the current state of broadband (quasi-monopolistic), some rural communities miss out on good broadband because, quite simply, rural broadband isn't profitable enough for the current broadband monopolies [1]. Frankly, good broadband makes a given location that much more attractive to potential employees and other people living in the area. It would seem like the Kochs would at best simply keep mum about a muni broadband fight, even if it didn't necessarily gel with core beliefs.
Instead, my best guess is that their "libertarian oriented" cause funding got tied into the network of old school broadband monoplies' desire to restrict competition by legal decree (not exactly a libertarian thought, but currently aligned with Republicans). Voila, via the magic of political coalitions, the Koch brothers now "provide" some of the funding for anti-muni broadband campaigns.
[1] http://www.roanoke.com/opinion/editorials/editorial-minnesot...