So what's the big deal? The big deal is that it forces those who run religious organizations to violate their fundamental religious beliefs--and Freedom of Religion is all about not being forced by government to violate fundamental religious beliefs.
To give an analogy, it would be like the government mandating that all delis, even Kosher delis, serve pork products and then justifying it by saying that protein is healthy, and many Jews who don't follow Kosher laws and many non-Jews go to those delis. The law wouldn't technically ban Jews from owning delis, but it would effectively ban their ability to run them according to their conscience. [from the article linked above]
In case you're thinking, "OK, but this mainly affects Catholics and I'm not Catholic (I'm not either), I would remind you of the saying attributed to Martin Niemoller describing those who did not stand up to the Nazi's:
First they came for the communists,
and I didn't speak out because I wasn't a communist.
Then they came for the trade unionists,
and I didn't speak out because I wasn't a trade unionist.
Then they came for the Jews,
and I didn't speak out because I wasn't a Jew.
Then they came for the Catholics,
and I didn't speak out because I was Protestant.
Then they came for me
and there was no one left to speak out for me.
More and more, the government is seeking to force religious organizations to hire people who behave in ways considered abominable to those organizations. More and more the government is seeking to force religious people, clinics and hospitals to perform abortions in violation of their consciences. More and more the government is seeking to force Christian adoption agencies, Christian psychologists and business people to violate their fundamental religious beliefs in the name of non-discrimination--all the while discriminating against people of faith by ignoring their Constitutional rights!
If people of faith do not unite and stand up to this tyranny, Freedom of Religion will eventually become so eroded and re-defined that it will come to mean, "Freedom of Worship" rather than "Freedom of Religion. In other words, "Freedom of Worship" will mean, "you have the freedom to worship within the confines of your home or church--as long as you do not criticize the government (there is already an IRS rule against criticizing politicians by name from the pulpit) and do not bring your religious views into the public square."
That's the kind of "Religious Freedom" they have in some Muslim and communist countries.