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But he did rule that burning the US flag was constitutionally protected free speech, but burning the cross was not.

“but burning the cross was not.”

If he did, I have no doubt it was in context of the KKK burning a cross, not a mooselimb.

"But he did rule that burning the US flag was constitutionally protected free speech, but burning the cross was not."

Not exactly. The case you're referring to is Virginia v. Black et al., 538 U.S. 343 (2003). Breyer joined the 7-2 majority, lead by O'Connor. Oyez has a good description of the central legal holding(s) of that case. It reads...

Question:
Does the Commonwealth of Virginia's cross-burning statute, which prohibits the burning of a cross with the intent of intimidating any person or group of persons, violate the First Amendment?
Conclusion:
Yes, but in a plurality opinion delivered by Justice Sandra Day O'Connor, the Court held that while a State, consistent with the First Amendment, may ban cross burning carried out with the intent to intimidate, in which four other justices joined, the provision in the Virginia statute treating any cross burning as prima facie evidence of intent to intimidate renders the statute unconstitutional in its current form, in which three other justices joined. Justice Antonin Scalia left the latter portion of the Court's conclusion to argue that the Court should vacate and remand the judgment of the Virginia Supreme Court with respect to Elliott and O'Mara, so that that court could have an opportunity to construe the cross-burning statute's prima-facie-evidence provision. Justice David H. Souter, joined by Justices Anthony M. Kennedy and Ruth Bader Ginsburg, concluded that the Virginia statute is unconstitutional and therefore concurred in the Court's judgment insofar as it affirmed the invalidation of Black's conviction. Justice Clarence Thomas dissented.

While I haven't been able to find the transcript from Breyer's conversation with Stehpi, it doesn't appear that Breyer referenced VA v. Black, but rather made mention of Oliver Wendell Holmes opinion in writing for a unanimous court in the very famous case, Schenck v. United States, 249 U.S. 47 (1919).

I could see an intellectual argument being made that recognizes a nexus between VA v. Black with respect to Koran burnings, but any nexus - implicit or explicit - with Schenck is laughable and frightening, all at the same time. Breyer's comments are most disturbing, and hopefully will be discussed at some length in the media.