( since white settlement ) we have been a Christian dominated society, various denominations have suffered some discrimination from other denominations, but as a whole Christians have enjoyed a position of privilege.
I would say this is evidenced further by the fact that there are some gaps in anti discrimination law in the protection of religious freedom, because for the most part anti discrimination law has been written to address specific recognised problems, and persecution of the religious simply hasn't been a problem requiring addressing.
Secularism isn't simply a separation of church and state, it's societal, and it's only quite recently ( relatively speaking ) that the desertion of religion has become more prevalent. So one could say that whist the laws have not changed, certainly society has, and all that has seen is the erosion of the position of privilege the religious have held over and above the secular.
That being the case, one could look at the way this legislation is designed to enshrine a hierarchy of rights, whereby the rights of the religious are given greater import over other basic human rights of the non religious, as a push back from the religious, not as means by which to ensure some form of balance, but indeed an effort to regain lost privilege.
This faux persecution argument is nothing but a lament for that loss.