Given that religion has frequently been the rationale for war, toleration has always been something of a delicate flower. Toleration of religious differences in Christian Europe and the Americas was hard won, but has become something of a central principle. The idea of separation of church and state was central to that, and overall it has been an amazing success, permitting the growth of a vibrant and largely tolerant society in the US and seemingly bringing the end - or nearly the end - of the long series of intra European wars.
Most large scale civilizations have managed to achieve a degree of toleration of diversity of belief, but given that the two big religions of the world, Islam and Christianity, both have a lot of built in intolerance, that has usually been at the expense of a tolerated but disadvantaged minority, as for example, has often been the case of Jews and Christians in Muslim society.
So how does a tolerated but intolerant minority survive in an alien culture with limited tolerance? Very carefully. Violence, proselytization, and other actions deemed threatening to the dominant religion have typically been harshly repressed, often by drastic collective punishments.
Islamic terror presents a tough challenge for any tolerant society. The historically traditional responses to something like the massacres in Paris would have been mob violence, with the slaughter of hundreds of the members of the religious group from which the terrorists came. The tradition of tolerance, we can hope, is now strongly enough established that that won't happen, but some sort of anti-immigrant, anti-Muslim reaction, including the possible triumph Le Pen's anti-immigrant and fascist tinged party is all too possible.