It's hard for me to answer that, because I don't consider the flag or the national anthem to be sacred and I'm not offended in the slightest by people who protest during the anthem or wear the flag or anything in between.
But I also know that many folks view things differently. And I think it's important to at least acknowledge their values and what they consider to be sacred.
The first analogy I thought of is when people draw Mohammad. Do they have a right to do that if they want? Sure. Should they be aware that doing so is offense to many Muslims? Absolutely.
Or perhaps if you're Christian, and you're attending a monthly BBQ with other Christians. Traditionally at this BBQ people say grace before anybody starts eating, and it's important to many of the attendees. If you make a point to eat something before they do that as some sign of protest, maybe you have that right. But should you not also be considering that doing so offends them? Is, "it doesn't bother me, that's not how I practice my faith" a reasonable response to their complaints?