because they are diffrent processes. Exactly for similar reasons people mix republic and democracy (which is an often employed rightwing/libertarian "argument" to justify non-democratic processes), when the two concepts have nothing to do with eachother.
Of course freedom of religion leads often to separation of Church and State. But it's not always the case. The UK has no separation of Church and State, but freedom of religion. Sweden has recently separated, but since they had state officials that were priests (state religion), some of them in the 90s refused to ordinate womenpriests thus violating other secular laws of non-discrimination. The guys were in an impossible seat : they had as civil-servants to enforce a law going against their beliefs. At the same time it was perfectly legal in Sweden to convert to any religion. There are several examples of the same kind in other European countries
So my reasoning is still valid. The separation of Church and State in the US isn't completely clear, because it's ONLY named as an expression of freedom of religion in the Constitution. Which leaves the door open to plenty of loopholes that the fundies use. For example Mormons claim that the 1st amendment would be violated if inquiries of molestation of children are made in Churches.
http://www.mormonstoday.com/000820/NGeneral.shtml. And I'll skip presidential oaths, public monuments, prayers in schools etc... which all together are a monumental attack against the very principle of separation of Church and State.
I quote : "that religious groups should not be able to use the government to persecute people who deviate from fundamentalist beliefs." Very nice....
from ANY belief, it should stand. It should not even come into question. Religion is a PRIVATE matter. Which doesn't mean that people can't have the right to have churches or do whatever they want EXCEPT if that goes against secular laws. The State must protect and enforce that right to practise a religion or not to. But religion can't never be a legal motive to justify an otherwise illegal action.
So democracy is a system that implies rights. One of these is freedom of religion. But without a clearly formulated principle of NON-NEGOTIABLE secularity and separation of Church and State inwritten in a constitution and applied consequentlty througout all legislation, that right will be rapidly eroded...
and it's exactly what's happening in the US today...