I am still on my long English campaign on default settings. To be honest, I hardly fight rebels.

I am around turn 90, I have lost a few units going rebellious, but for about 10 turns I was excommunicated due to a bug.

You should check all your settlement details, maybe the french started with alot of unrest, I dont know.

Build an inn and start plopping out some spies and move them to your own cities and see if they can uncover any foreign spies that could be increasing unrest.

Right now most of my front line has at least 2 spies in them and its amusing watching them die trying to plant someone.

But as to why you have so many rebels, all I can figure is check settlement details and see if it provides clues. Like I said, I had very minor time with rebels and was actually missing them to provide some experience.

I havent even seen an inquistor yet, and 1 witch. Of course one I get the details all down going to start doing H to VH settings.