I'm not appealing to the court's authority. So that you and others can see the reasoning, I'm pointing you at a carefully-considered legal opinion by a federal judge. One similar to others on the topic, like Judge Walker's decision on Prop 8. Hand-wave it away if you like, but the rational-basis standard [1] is a key legal concept here.
When court after court finds that there is no rational basis to these laws after carefully examining every rationale offered by proponents, I think it's reasonable for gay people to conclude that promoters of those laws are irrationally biased against them. Especially those promoters unwilling to offer any other explanation.
Except the "proponents" in this case did not include the people who put forward this referendum in the first place. Instead, the referendum bypassed the California government to put the issue to a popular vote. When the popular vote was challenged in court, the government lawyers had no incentive to put up a good defense, which they didn't.
It's really a loophole in the referendum system, and if California is serious about the referendum, they need to give standing to some groups to give them the right to defend their initiatives in court.
Even if you were right, that wouldn't be the case for the Michigan case I linked upthread, where state officials stood firmly behind keeping gay people from marriage.
"The Supreme Court decided the case on the basis of lack of standing."
...meaning the proponents weren't allowed to defend it in court.
I've already stated my feelings about the ruling in the Michigan. In fact, I have deep misgivings about the kind of research presented in that case on both sides, especially when it comes to making policy decisions.
The proponents did defend it in federal court. They lost.
It's true that the Supreme Court wasn't interesting in hearing from them again, but there is absolutely nothing to suggest that if they had, it would have turned out as anything different than their disastrous showing in federal court. Remember, they were going to the Supreme Court seeking appeal, which means they don't get to re-litigate the whole thing, just to raise questions about particular points of law. The findings of fact would stand, and as far as facts went, they had nothing.
When court after court finds that there is no rational basis to these laws after carefully examining every rationale offered by proponents, I think it's reasonable for gay people to conclude that promoters of those laws are irrationally biased against them. Especially those promoters unwilling to offer any other explanation.
[1] http://en.wikipedia.org/wiki/Rational_basis_review