You are showing great wisdom in doing your pre-trip homework. The port of Civitavecchia is about 1:15 min from Rome on either a bus or the train. The buses are similar to chartered-type buses found in the US... which means they are clean, have AC, and our pretty comfortable. Some have bathrooms and some do not, so its hard to plan based on this issue. The quality of the trains really does vary from the older commuter type trains with no AC to very modern high speed intercity trains that are better than anything you will find in the USA. From Civitavecchia to Rome the trains are generally not the best, and can often be very crowded in the early morning which is when many cruise passengers are trying to get to Rome. All the trains do have toilets,..although sometimes they leave much to be desired. In Civitavecchia its possible to take the free shuttle bus from the pier to the port entrance...and from there its about a 10 min walk to the train station. Traveling in Western Europe is similar to traveling in the US which means you can use tours, hire private guides, or do things on your own.