I just picked up a rental car in Palermo in May 2014. We used Kemwel, and found that they had a MUCH cheaper rate than either AutoEurope (their sister company) or Gemut. For us, the non-negotiables were an automatic transmission, zero deductible, and a car large enough to hold all our luggage out of sight in the trunk. Our rental ended up being from Hertz, and our car ended up being a Fiat 500L, which turned out to have a trunk area just large enough for all our stuff; we were very glad we didn't get a smaller car, even though there were just two of us.
For our particular rental, it ended up being cheaper from the city location rather than the airport. Of course, we were worried about getting out of town, but to get from the Hertz office to the highway turned out to involve only a few turns and a few surface roads. The one thing that everyone in Palermo agreed on was that we should not try to drive through the old part of town, and fortunately this was not at all necessary.
If you want more details about my trip to Sicily, here's my report: https://community.ricksteves.com/travel-forum/trip-reports/sicily-palermo-caltanisetta-siracusa-taormina.
Note that I still haven't finished it, so do check back for updates, or PM me if you have questions.