This is a long opinion, and entails an elaborate discussion of the Establishment Clause as applied to a fairly unique set of facts. If you're interested in conflicts between Church and State, reading the whole thing is time well spent.
That said, I can summarize the dozens of pages of single-spaced text fairly concisely.
Here's Judge Paez, who authors the majority opinion: "It's okay for San Francisco to pass a totally symbolic resolution that says that Catholic Charities shouldn't discriminate against gays and lesbians by refusing to place adoptive children in single-sex families, even though Cardinal Levada said they should. That's just San Francisco's take on a matter of public interest. A City can speak on a secular subject even when doing so insults the policies of a particular Church."
Here's Judge Berzon, who concurs: "I agree with Judge Paez. I just want to add that I'm a little nervous. It's okay here, sure. But were the City to go farther -- start taking out advertisements to slamming the Church, start telling Muslims not to observe Ramadan, etc. -- and we're looking at something different. Tread lightly."
I think both opinions are well put. For myself, I've got no doubt that an American Kristallnacht -- or anything like it -- would violate the First Amendment. But I also agree that this ain't that.