The best reason to permit others to burn effigies and crosses is that once they do they are exposed for who and what they are. And once exposed we can ridicule and make such a stance impossible to hold in wider soceity. The roots of that hatred will have an exceedingly hard time taking root. Look at the flourishing of Westbrough Church as evidence. If we were punitive and impeded the rights of Westbrough to protest and exercise their speech they wouldn't just be a troubled little family church - they'd be the mormon church.
I get it's not comfortable to see a group of people belittling your experience as a person, or protesting your existence, or demanding your rights be taken away. One could feel, justifiably, threatened by such actions. However, it is a necessary condition of free speech that such hateful and odious speech be protected, and protected at all costs. This means people will feel objectified, trivialized, maligned, and at times afraid.
Just because we are at a place right now where the majority of people wouldn't consider a black man or woman voicing their displeasure with the speech of white people burning crosses to be anathema to a functional society, doesn't mean it will always be that way. It was freedom of speech that fuelled the abolition movement. An argument could have been made then that abolitionism were practising hate speech. One could argue the constitution is hate speech.
Don't take any of this the wrong way. I don't endorse or support the views of people who would take such actions. I support their right to do so. Not for some abstract reason, but because I want to freely speak my mind when and if what I have to say makes others uncomfortable AND being an atheist automatically places me firmly in a group of people who are the least respected, least loved and least trusted.