I agree with Sanchez and Patashnik that there's no necessary contradiction between Obama's nominal opposition to same-sex marriage and opposition to the California Restoration of Bigotry initiative. As I think I mentioned before, Dan Pinello found a significant number of Massachusetts legislators who didn't initially support same-sex marriage rights but was opposed to repealing them once granted. Obama's position isn't terribly surprising or unusual, and nor is it incoherent on its face.
Still, I also agree with Matt that while this position is a coherent rationalization of his stated views, something simpler is probably going on. Obama probably supports same-sex marriage but doesn't feel he can express this view while trying to hold a national coalition together.
And while people often focus on the backlash successful litigation provokes among hostile to same-sex marriage, there's another side to it: litigation also makes voting against same-sex marriage more difficult and provides political cover for politicians who would like to support it but are reluctant to support changes in legislation. In addition, having same-sex marriage is instituted in even a few states without the hysterically anticipated social apocalypse makes arguments against it harder to sustain.
At any rate, Obama's subjective beliefs aren't really important. As same-sex marriage becomes more popular Democratic politicians will support it in greater numbers.
--Scott Lemieux