In part because there's no "truth-o-meter" to detect whether they're merely claiming religious belief to justify their bigotry.

The other part is that "prejudice based on a religious belief" has NEVER been -- directly -- acceptable because in much of American history the prejudice has been justified by non-religious reasons.  Those reasons have now been shut down. Religion is the last refuge of bigoted scoundrels.

It is over-(and mis-)used as a phrase but here it is literally true: there is NO PRECEDENT for an invocation of religious rights to deny OTHERS their constitutionally protected rights. Religious freedom is about protecting a right to worship free of governmental influence. It is not a "do whatever you want to do to others" permission slip.