Quote Originally Posted by Slug For A Butt
The only places I don't really use them is against Cities (waste of time, you'll not lower the order enough for a rebellion and you won't make that much difference to the income) and Inquisitors (the Pope will hate you when he gets wind of it).
In previous campaigns, I used them quite a bit with cities. Destroying economic buildings might not necessarily reduce the factions income, but it does start to take a toll on the enemy if they need to constantly spend money to repair their buildings. In addition, take out their castle recruitment buildings and you slow down the ability of the AI to recruit/retrain troops.

After waging this economic warfare I managed to bring several factions to a halt where they just were not producing troops or able to repair their buildings. With that said, I've had squads of 4-5 assassins going after several buildings a turn, so a concentrated assault can make a difference.

What it comes down to is playing style.