The drive from San Jose to Quepos is 170 km and takes 2 1/2 to 3 1/2 hours, depending on the traffic. Expect a slow drive, the maximum speed limit in Costa RIca is 80km/hr.
There are a wide variety of rental car companies. Basic personal liability insurance is required to be purchased at the rental car company in Costa Rica, and is usually not included in the quote you may have received. Car damage insurance may be purchased separately, but your credit card, if used to pay for the car rental, likely will cover this. Check with your credit card and bring a copy of the policy - saving you from buying this additional insurance at a significant cost.
If you are coming to Manuel Antonio you don't need a 4x4, as the highways are good. A costly 4x4 is only needed if traveling off the beaten track. Cars can also be rented in Quepos/Manuel Antonio from all the major car rental companies, which saves you from having to drive thru the busy/confusing San Jose area traffic.
DO YOU NEED A CAR FOR GETTING AROUND MANUEL ANTONIO?
While in Manuel Antonio you don' really need a car if you don't mind walking, using the good and cheap local bus system (really one route along the 5 kilometer road between Quepos and the national park), using 1 of the many cabs, or using hotel vans from the larger hotels.