As the article mentioned, the scary part of this technology isn't the technology itself - it is the potential applications of the technology. Any openness coming from a company with an application like this is a positive market pressure.
I'm perfectly fine (and I think most people would be) with certain applications being throttled (to a reasonable extent) as long as I am told up front about it in my ToS, and as long as I know that my data is not being stored anywhere.
A first step to that kind of trustworthiness is more openness as to the filtering software being used.