Do religious practices require special protection? If history is any indication, unfortunately, yes - cultural/religious genocide attempts against indigenous peoples in particular has been far too common for me to say otherwise. Right now, a case is being considered that will rip children from their indigenous families and rob them of the ability to learn their cultural/religious traditions from the tribe. Without special consideration of cultural/religious elements - because goodness knows the Untied States can't be bothered to give much respect to the sovereignty of the First Nations - I'm not optimistic about how this case will be ruled by the current SCOTUS.
I'm not sure why this equates to religion needing special protection. You only really spoke to religion as an aspect of culture.
Is the religion of indigenous people more important than, say, their language or their traditional skills?