The ruling merely says that churches can't be discriminated against by a State government just because they are a church.  

So the 80% plus of the people in this country who claim some religion can't be discriminated against by the atheists or the agnostics.  

SCOTUS is the final arbiter of the law; they aren't supposed to get out of the way; they are supposed to decide!

They do defer to the Congress and they do defer to the President.  The Constitution requires that in some instances.

But in the end, they Decide what the law is!  Not what it ought to be; not what a majority or a minority would like it to be (or even vote for it to be) but what it is!