In the US, the US flag is the only one that had any protection from desecration, and that was what the SCOTUS decision addressed, finding that desecrating the flag as a political statement is protected speech. No other country’s flag has ever had protection. OP’s statement is comparing apples to oranges. Vandalizing a US flag that is not yours is still a property crime. Vandalizing the Israeli flag at their embassy is also a property crime. But if you’re shouting Jewish slurs as you do it, that activates the hate crime enhancements.

If you just stand outside the embassy and yell slurs, that’s not illegal. But when a crime is committed and the motivation involves race or religion - that’s when the penalty for the crime increases under the hate crime law.