In a judgment handed down on Tuesday, the European Court of Human Rights rejected a claim brought by a Muslim couple in Basel, Switzerland, who had refused to allow their daughters to attend compulsory mixed swimming lessons at school.

The ruling itself is unsurprising, and doesn't come in a vacuum. The European court has been called upon to weigh in on issues of religious freedom before - and a pattern has emerged, which is difficult to ignore.

Two basic trends have materialised - the first is one where the court has adopted a more neutral kind of secularism, and where the judges have prioritised the individual consciences of the plaintiffs over that of the different authorities that, invariably, call to notions of "public order" to justify certain restrictions.

But this trend has typically been associated with religious freedom cases lodged by members of Christian communities, including, for example, the British Airways employee who had been told by her employers that she couldn't wear a crucifix. Indeed, even state authorities have, in order to protect a visible manifestation of Christian heritage, appealed to the court to allow for crosses to be openly displayed in state schools - and were successful in doing so.

There is, nevertheless, another trend at work - one which is far more aggressively secularist, and which has, invariably, affected Muslim communities. French and Turkish citizens have applied to the court to protect their right to use certain types of clothing - particularly the head-scarf or hijab and the face veil or niqab.

In light of such cases, as a former employee of the European Court has pointed out: "… some consider that the Court has more frequently sustained a form of strict secularism, or even a sort of intolerant secularism or enlightenment fundamentalism. This is especially so in cases when individual religious manifestations do not display any signs of political intentions but are performed bona fide making these prohibitions difficult to reconcile with the necessity to protect a democratic society."

'Social integration'

In that trend, the court has prioritised the state's rights over individual freedom of conscience - to the point where it seems that the court has taken the state's arguments around what it considers as legitimate aims as a given.

It's not quite clear cut, though. In this particular case, the girls were children - they hadn't even met the age of puberty - and the school had said that a full length wetsuit, popularly known as a "burkini", could be worn. One would have thought that a compromise might have been found. But the precedent has now been set - and the court is clear.

How 'social integration' is served by forcing families to put their children into a very specific type of sporting activity - one that only a few years ago would have been segregated according to gender in many European countries - is unclear.

Burkini, no burkini - below or above the age of puberty - it seems that Muslim parents who wish to withdraw their children from mixed swimming lessons will be unable to do so.

The ramifications of the case are more than just a swimming lesson issue. The reasoning mentioned by the court enshrines much more than that. It claimed, in a rather sweeping statement, that Switzerland's right to facilitate "successful social integration according to local customs and mores" took precedence.

Further, "The Court observed that school played a special role in the process of social integration, and one that was all the more decisive where pupils of foreign origin were concerned," the statement read.

It's a very sensitive and delicate argument - and not one made very well by the court in this regard. How "social integration" is served by forcing families to put their children into a very specific type of sporting activity - one that only a few years ago would have been segregated according to gender in many European countries - is unclear.

Islam in Europe

It is difficult, also, to separate this ruling from the wider anti-Muslim sentiment in terms of "visible Muslim-ness" across Europe. Remember: Switzerland was the country where a few years ago a national referendum was held on mosque minarets (though there were barely any minarets in the country) - and the Swiss banned minarets as a result.

But this isn't simply about the Swiss - generally a tolerant nation and accepting of diversity - far from it. The Swiss are part of a wider discussion, where three things are being hammered out across Europe. The first is how to recognise religion in an increasingly secularised Europe, a continent where there are now only eight recognised state-churches. Norway, for example, just disestablished their own national church a few weeks ago. Religion is no longer considered as important in the national sphere in most European countries as it once was.

Secondly, how is Europe to acknowledge Islam as a religion in the European public sphere? There is a great deal of resistance to that, historically and today, but whether we like it or not, Islam is a European religion, and its adherents are not excluded from being European just because they are Muslim. Europe as a whole has to come to grips with that.

Finally, how does Europe incorporate Muslims as individuals and as communities, visible ones or not, even when they are different from what is now more commonly acceptable? Even when reluctance to engage in mixed-gender sports has only recently went "out of vogue"?

Where does it end and who decides? Are Muslim Europeans actors in that decision, with as much a European voice as any other European? Or are they simply subjects to be told that this is the way it is and if they don't like it, their European-ness is rejected and they can "leave"? To where, nobody knows because, like it or not, they are Europeans.

All of that is taking place against the backdrop of major issues such as terrorism and migration - and while these should be segmented out, they're not going to be. The fears of Eurarabia remain, as preposterous as they may be.

Right-wing populists - and even many on the left - make a good deal of political hay on these issues. That is very likely to continue - and, alas, this court ruling just makes the situation all the more difficult.

Europe is going through a very challenging period and Muslims and non-Muslims alike need to be creative about how best to move forward. This latest outcome isn't a good example of that at all.

Dr HA Hellyer is senior non-resident fellow at the RH Centre for the Middle East at the Atlantic Council and at the Royal United Services Institute in London. He is also author of "The 'Other' Europeans: Muslims of Europe".

The views expressed in this article are the author's own and do not necessarily reflect Al Jazeera's editorial policy.