The obvious question that hits first when looking at the recent furore over whether a church-run adoption agency should be allowed to apply its religious principles in a manner that would be illegal for anyone else, is: Why on earth should a church have special privileges?
It is quite common for governments to allocate privileges to religion. It's difficult at first to see why this should be. Of course, it might be logical to privilege one specific religion, if that one is believed to be "true". However, that logic cannot account for generic religious privileges. The lack of underlying logic to the position is exposed by those playing with the boundary of what constitutes a religion (via Volokh.)
Looking at the question historically, the answer is immediately obvious: religions get extra freedoms, because when they don't, they fight. The lesson of history is, that you can take away all sorts of freedom with impunity, but if you obstruct people observing their religion, you're risking violent resistance.
If you see politics, as I do, as a compromise between interests (rather than, say, a search for Justice), then this situation is OK. A preference that is held strongly enough to arouse violence is more important than one which is not. (Irrespective of the objective merit of the preference). There is a long-term issue that this attitude is encouraging violence, but that is very long-term in this situation, where the deference to religion in itself has grown over centuries. Responding promptly to violence, such as that of the animal rights movement, would be much more problematic than this slow adaptation to the existence of potentially violent religious movements.
The same incentive problem applies to rolling back the by now time-honoured privileges of religion. If we reason that because the Catholic / gay adoption issue isn't likely to turn violent, we don't need to worry, then we're penalising peaceability. This concern is highlighted by the recent YouTube spat where a prominent atheist who has long published criticisms of Christianity is banned as soon as he starts making similar criticisms of Islam.
On the other hand, if new movements seek to claim the time-honoured status of religion, it is reasonable to ascertain whether they are "real" religions according to the only criterion that matters - whether they are likely to eventually turn violent. Therefore, our new Muslim communities succeed, and the Jedi of Brighton and the Brethren of Georgetown fail.