The French Wars of Religion lasted for nearly 40 years. By the standards of a civil war, this must count as one of the longest.
No-one side had the ability to end the wars quickly. The military clout of both sides was not great so that no one war witnessed a decisive blow. That meant both sides could recover sufficiently to continue fighting given a suitable break. As war at this time was regional one specific area of France may have been at war and the rest of France may not have experienced the impact at all so that there was always a region capable of a war in that the men and equipment were available. The wars never affected the whole of France at any one time and though one area may have been incapable of continuing fighting there were others that could do so.
Also the lack of mobility made wars very regional and condensed. The wars themselves were never of such intensity as to fully destroy an opponent and some of the wars were wars in name but not in reality. The Seventh War - the so-called "Lovers War" - was and is classed as a war within this civil war but in reality it was nothing of the sort and other wars can also be suitably classed as such. The nine wars can really be narrowed down to two major wars (the third and eighth) whereby damage was done to both sides but there was sufficient time for both to recover and continue fighting. The ninth war technically lasted nine years but the majority of those years were spent fighting foreign powers (primarily Spain) and so cannot be classed as part of the civil war known as the French Wars of Religion. In fact the campaign against Spain probably gained Henry IV even more support as Spain was seen as the traditional enemy of France and loyalty to the legal monarch who was now catholic was common throughout France.
In this sense, the civil wars ended earlier than the date 1598 might suggest. The campaign against Mercoeur lasted until 1598 BUT it can be argued that this was a very specific action against one noble faction rather than a civil war. However, a counter-argument to this would be that such disloyalty to the monarch was all part of the process of the civil war and this campaign against Mercoeur was simply the end part of it and that it was characterised by the classic symptom of French politics in the C16 which was the king advancing his power at the expense of the nobility with the nobility attempting to counter this.
Another reason why the wars lasted so long is the fact that anger was so deeply entrenched.
After the Massacre of 1572 the Huguenots realised that any fight would almost certainly be to the end and that negotiation was all but out of the question. Hence their continual part in the wars. Likewise the catholic involvement as exemplified on the part of the Guise family made reconciliation all but impossible.
With these lines drawn as such each side had to fight for its own survival and with the Catholics accounting for 90%+ of the population the Huguenots had to assume that any challenge made to their survival had to be matched with a desire to fight for their survival and this would involve them in any potential hostile action which the Catholics were perceived to be engaging in and which would have to be met by a hostile response.
Such was the deep seated bigotry of, on this occasion, the Catholics that any form of understanding and acceptance of the Huguenots was all but impossible. The celebration of the massacre in the catholic states of Europe (done at the behest of the pope) gives a clear indication of the failure or refusal of one side to accept the other and that mean that for one side the wars were wars to ensure the survival of their faith against heresy, while for the Huguenots the wars were fought simply for survival.
"Sixth French War of Religion". HistoryLearningSite.co.uk. 2006. Web.