When searching 3 day economy car rentals for Italy in April via either US or European web sites it shows a reasonable daily price of $65 or so then a total due at time of rental for over $1000! Am I missing something??
Have you tried Auto Europe, they have the reputation among travelers here for consistently having competitive pricing: http://www.autoeurope.com/carsplash.cfm?aff=RICKSTEVES
I couldn't get as low as $65/day checking Autoeurope, but found rates not much higher. The sites you are searching may be asking for some sort of security deposit to be held on your credit card. Check out Autoeurope and then call their 800 number in Maine with any questions. Their phone staff is very halpful.
It is hard to know without looking at the site what you may be missing. Some things to look for:
Where are you picking up the car. If it is at an airport or a train station this can add hefty fees.
What insurances are being added to the daily rate. I have never rented in Italy, but I have heard that the laws there require some insurances that are not required in other European countries. Usually Liability is included in the daily fee wherever you rent. Are other insurances being tacked on?
Is your pick up and drop off location the same? This can also add fees. If all else fails, find a toll free number and call and ask for an explanation. In my experience, if the rate is super low, there is usually a built in expense not showing in it. However, $65.00 a day does not seem super low to me. Let us know if you ever figure it out. (And help further my own travel education)
When I searched for a low rate in Germany, I found Sixt.com the best. Search their page to see if they rent in Italy. It might depend on which cities you will drive in.
I suggest using the toll free phone number and talking with an agent. $1000 definitely sounds too high for 3 days! Read on this page what others have experienced. See "Driving Europe Crazy".
Check to see if there is a minimum rental period. The last time I tried to rent a car for only three days, I was told I would be charged for a week because that was the minimum time.