This isn't a total surprise, as the FCC hasn't hidden the fact that it doesn't agree with everything that Google and Verizon have proposed. The commission released a public notice back in September taking issue with two aspects of the Google-Verizon proposal.
Genachowski conceded that it was ultimately positive that two companies like Google and Verizon were willing to work together to try to help unwrinkle the policy quagmire that is net neutrality, but he seemed to take issue with the way the proposal was approached.
The FCC isn't the only group that has criticized aspects of the Google-Verizon proposal, and in truth, that seems to be part of the problem. Beyond any genuine policy questions or disagreements the commission may have with the proposal, its mere existence made the already muddled and confusing debate regarding net neutrality that much less clear.