Libertarians support the peaceable free exercise of religion, and the separation of church and state. (And the separation of just about everything else and state, for that matter.) When religions attempt to legislate their beliefs, or commit violence, they are no longer peacably exercising their rights, but violating others' rights.
Falun Gong Human Rights
Working Group: describes the horrific torture and persecution
inflicted on Falun Gong practicioners in China
Witches' League for
Public Awareness: an extensive pagan/Craft site
including case studies of attempts at limiting unpopular
religions
Essays by
Gene Garman on the separation of church and state