From my perspective this question is rather difficult because either way someone's rights get trampled. I firmly believe in the right of freedom of choice for women regarding all aspects of women's health and in particular contraception and abortion.
However that being said I also believe in the right of a business to make decisions about how their business is conducted and how it treats its employees from a benefit stand point. The key factor here is when that business is "closely held" meaning that it is not that far removed from a family owned business operation.
This really goes back to the old discussion about racial discrimination in which businesses could no longer operate if they refused to provide service or product to other races. In this case though it only involves the employees of these firms and they have the option of simply not working there if their beliefs do not coincide with those of the owner/operator.
In every case of social differences, whether it be on the women's rights issue, the LBGT issue, racial issues, other religious issues, or what have you there will always be those who feel as if they are being discriminated against no matter how the questions are resolved. That is the plight of living in a free society where generally the majority rules.
Now when it comes to large corporations that is when this whole issue kind of comes apart. That is because in any large corporation you will have a virtual cross section of beliefs for a given society. In order for things to be completely fair and equitable then the option of free choice rests I think with the employees and should not be governed by the corporate heads personal beliefs.
I also feel the same way about governmental "executive orders" where a president can inflict his personal beliefs upon an entire nation at will. Such was the case when Pres. Geo. H.W. Bush denied federal funding for stem cell research on the grounds of his personal religious beliefs. That was blatant discrimination against all people who had no problems with such research and in fact were in need of it for their own personal issues.
In my case my late wife was diagnosed with Parkinson's disease in 1998 and died from complications of that disease in 2008. That was almost the precise time that stem cell funding was cut off in this country and at the time such research was and still is the best hope for any progress with many neurological disorders and injuries to the nervous system.
The bottom line here is that freedom comes with a price and sometimes that price is having to accept the will of the majority. It is a bit like speed limits. They are established to meet the capabilities of the least capable driver but hardly anyone adheres to them because they usually feel that their experience level is higher and they are more capable of maintaining control and higher speeds. Consequently when they are ticketed for speeding they feel as if they are being unfairly persecuted when in point of fact they did indeed break the law.
So this is where we have to be careful when administering blanket rulings about such social issues. It is not a "one size fits all" kind of question in most cases and the women's rights issue regarding birth control is just such a case. This is due to a number of reasons that include religion, individual morality, emotional issues, and even economics. The idea is to find the best possible common ground in such issues.
So in this case I agree that small privately held companies should have the right to request exemption in such cases while large corporate and publicly held companies should follow the majority rule within a society. Since Hobby Lobby is a publicly held company frankly it should be held to the same measure as any other publicly held company and this rather sets a precedent for any company to reject certain aspects of a health care plan based upon their internal beliefs. To me that is wrong so I am inclined to disagree with the court on this one.