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Planes, trains, and automobiles are all options when deciding on a mode of transportation to get you to Assisi. Most visitors find it easiest to travel via rail; in general, rail travel is fast (although, well, fast can be a relative term in Italy, especially if you're coming from super-efficient Switzerland), convenient, and very backpacker-friendly.
There are three airports that serve central Italy. Flying into the Leonardo da Vinci or Fiumicino Airport in Rome may be your best bet. A number of airlines provide direct non-stop service to Rome. Once you arrive in Rome, you may either rent a car or take one of several buses or trains to Assisi. Another option is to fly into Pisa. Sixteen airlines provide domestic and international service to Galileo Galilei International Airport. Like Rome, you can choose to either rent a car or take the train or bus to Assisi from Pisa. A third option is to fly into Florence. A number of airlines provide domestic and international service to Aeroporto A. Vespucci, also known as Peretola. Trains to Assisi are readily available from Florence.
Assisi is easily accessible by rail. Just ensure before your travels that the day you plan to travel on doesn't coincide with one of Italy's indiscriminate transit strikes. If traveling from Rome, take one of the daily trains to Ancona and get off Foligno (about a tw-hour ride), where you will want to transfer to the train headed toward Perugia (about 15 minutes). If traveling from Florence, take the train heading toward Terontola/Cortona (about 1.5 hours) and transfer to a connecting train headed toward Assisi/S. Maria degli Angeli (about an hour's ride). Check Tren Italia's website for updated timetable information.
With its landlocked location, there is no worry of having to drive on cliff-clinging windy roads to get to Assisi (well, unless your starting location is on the coast, that is). Driving directions are pretty straight-forward. Rental cars are available from most major cities including Rome, Pisa, and Florence among others.