"Suppose I said that Mohammed was a child molestor, and a Muslim citizen overheard and broke several of my limbs in response."
If I went to a Muslim funeral yelling Mohammed was a child molester, I'd deserve to get my ass kicked. You see some free speech right issue here?
Yes, I do. People have a right to express unpopular opinions without being physically assaulted. Violence is only justified for self-defense. Saying something stupid, hateful, or evil does not threaten someone's safety, so violent self-defense does not apply.
I'm not saying that I don't understand why someone would assault a protester at a funeral. I can't even say I wouldn't lose control and lash out violently at someone protesting at a loved one's funeral. I do recognize that attacking the protester is not the right thing to do.