From my experience, there are two possibilities with inquisitors: 1) the inquisitors have been dispatched into your lands, and 2) the inquisitors are in other factions (possibly former) lands and you just inherited their presence. The first generally only happens when you are both not on the good side of the Pope and have a high amount of heresy. If you keep heresy under control and keep your relationship with the Pope up near the top, inquisitors will never head into your lands looking for you specifically. It's the second case that causes problems.

A lot of times, the inquisitors went there because the AI faction let heresy spiral out of control, or else got on the Pope's bad side. Occasionally the inquisitors will pass through your lands on the way to someplace else. The trouble is that the inquisitors ARE random. If there are targets within range, it seems they just check randomly for each to decide if they are going to try that target for heresy. It doesn't seem to matter what faction the target belongs to, its piety, standing with the Pope or anything else. I had some problems like this early in my Venice game. The pope was sending out inquisitors after the HRE and the French, but they burned a few priests and a couple of generals of mine on the way through.

The best suggestion I can make is to combine all the tactics: stay on the good side of the pope, keep your valuable generals away from where the inquisitors are located, squish them with armies, and put down heresy in your own lands. I'll add one of my own: keep priests around where the inquisitors are. They seem to burn priests before generals, as long as the priest is closer.