The BoR says nothing about how the government should treat religions comparatively.  All of the Rights in the BoR are prohibitions on the government's interference with the People's rights to do certain things.  Heck, the government could choose to fund just Islam and the President and Congress could pray to Mecca all day.  As long as that doesn't stop you from doing your Catholic thing, it's all good.

This isn't about government being fair (that's not the government's job).