While my faction leader is usually someone with high dread (due to assassinations and espionage), I don't think that this has an influence on nationwide unrest, as he doesn't have a trait that states something like that. Excomm or taxes aren't causing the 15% unrest as they are different types of negative public order.
Excomm has its own symbol (crossed cross) and high taxes have the bag with arrow symbol. I'm talking about the pitchfork with fire symbol though.

I experienced it both as turks and as milan, both times after a certain playtime (varied), and usually when I started having a lot of territories.

I appreciate the responses so far though, and wonder whether anyone else has had that problem?