People don't get prosecuted for their religious beliefs, but for using those beliefs as a shield when accused of violating the rights of others. Freedom of religion doesn't include the freedom to force anyone else to adhere to the same beliefs - it is precisely that which it exists to guard against.
Can you cite a case where someone was prosecuted without having affected anyone else's rights?
What about when the government affects our rights? Like using the force of law to force someone to sell a product, or not sell a product, that they don't wish too? Why is it that IF a person believes that "gay marriage" is immoral that the government has the "RIGHT" to FORCE them to sell that wedding?
It is NOT as simple as "DO AS YOU ARE TOLD". ALL beliefs must be respected, or none.
As I stated before, I have VERY mixed feelings on this. I abhor most, not all, types of discrimination, but I hold dear the RIGHT of each individual to run his/her/it's business as they see fit. WITHOUT the interference of government.