Politicking, News Media Sensationalism, Advantage Taking Advocacy Groups at their best. Follow the money.
Take all the above away and there is a lot of interesting interplay between different constitutionally granted protections here. 1st amendment, 14 amendment, civil rights legislation, etc.
A more than 20 year old concept originally designed to prevent erosion of the 1st amendment now with the new twist of potential discrimination against sexual orientation and other non-protected classes.
I'm not sure about all the scenarios, but don't think it will/can be legal to discriminate against classes of individuals already granted protection in the constitution, amendments and civil rights legislation.
The test, in the federal law - not sure about Indiana, is if an individual has a sincerely held religious belief (another topic is expansion religious freedom from individuals to privately help corporations)
PLUS
exercising that belief doesn't compete with an already established compelling governmental interest (like discrimination against protected classes) PLUS there is no less restrictive way to interfere with that religious belief.
So there are limits to what can be claimed as an exercise of religious freedoms (keeping lawyers, legislatures, judicial systems in business for years to come)
Likely ultimately heading towards the establishment of new protected class for sexual orientation/LBGT somewhere down the road.
Media companies will make lot's of advertising money running the stories, lawyers will make lot's of money litigating, Advocacy groups will make lot's of money from contributions.
And the most extreme people will get attention for voicing their opinions one 3 second sound bite or Twitter post at a time.
Now what about discrimination against fat dudes at all you can eat restaurants - outrageous!!!