It's not clear at the moment whether or not this includes people who have premium paid memberships or free memberships as well, or if more viewers will be able to watch the doc after that for a small fee. As of the time of this writing, the English Nico Nico Douga site doesn't have any more information on it.
Reuters reports that the documentary's Japanese distributor Unplugged canceled the screenings due to "fears that protests might inconvenience moviegoers." Unplugged's offices have been harassed, and protests have even taken place outside of Unplugged CEO Takeshi Kato, which you can read more about here. Kato told the AFP, "People discussing the film on the Internet are talking without having watched it, and it seems they don't understand its meaning...It's okay to support or oppose the film, but we hope that will be discussed after people watch the film."
Anyone who has seen The Cove knows how dangerous of a topic this is, although I think that the excuse of the theaters that it would merely inconvenience viewers is weak at best. Why not just come out and say that they fear boycotts, vandalism, violence against its employees, or worse? In any case, it is great that Unplugged is standing behind The Cove despite its controversy and the threats that have been made against the company and its employees, and that it's working fervently to make the film as accessible as possible to its audience.