First, a disclaimer, my knowledge is mainly limited to European wars of religion rather than historical animosity between Sunni and Shia so I will concentrate on the wars currently happening in the Islamic world (not that I would pretend to understand them in any great detail)

That said, it does seem to me that parallels can be found between the Protestant/Catholic conflicts of the 16th/17th century and the ongoing Sunni/Shia conflicts.

Both featured two seemingly contradictory aspects, the eschatological (relating to the apocalypse or end of the temporal world) and the political.

Just as many in ISIS do now, there were early modern Protestants who strongly believed their struggle with Catholicism was part of an apocalyptic conflict with the Antichrist. Nor was this limited to Catholicism, ever shifting ecclesiology and political circumstances lead various Protestant groups to label others as Antichrist at different times.

There were also though, huge political dimensions to the conflicts, the most striking example being the Thirty Years War, which was both a religious conflict and a geopolitical stuggle between France and the Hapsburgs, just as the current wars in the middle east are both religious wars and struggles for influence between US/Russia, Saudi/Iran.

Similarly, the wars of Protestant England and later Britain against Catholic enemies were often seen not as a religious crusade, but as a protection of liberal values inherent to Protestantism against absolutist, tyrannical values inherent to Catholicism. Individual mistrust of Catholics in Protestant England was also often justified on the grounds that they owed ultimate political allegiance to Rome, thus making them politically untrustworthy.

This can be seen even in the case of ISIS, which one would expect to see as the most clearly religiously motivated organisation involved in the current conflicts. Despite this, it is well documented that they have found support among members of the secular Baath party seeking to reclaim influence from political Shia that they feel has supplanted them. In a similar way, undoubtedly convicted religious radicals during the English Civil War made common cause with more secular republicans.