Traveling by train from Savannah GA to Charleston SC

The drive between the two cities is only two hours, and as with the U.S. in general, gasoline is extremely inexpensive compared to most of the world, and the road network is extensive and reasonably well-maintained, so the vast majority of people with access to a car will drive this route. I agree with you, however, that once you arrive, it will be a hassle to drive around the crowded historic core and to find parking. If traveling solo, I would certainly consider Amtrak or one of the bus options.

Most people would find any Amtrak experience far more comfortable than flying economy or taking a long-distance bus. There is no security screening. The seats are wider, with considerably greater legroom, with an electrical outlet for every seat. The restrooms aboard are larger. There is almost never a fight over luggage storage. The train is large enough that you can get up to walk around to stretch your legs, and there will often be a cafe car or lounge where you can sit at a booth to socialize.

Reliability can be a concern. According to the Amtrak Status Maps Archive Database (ASMAD), the morning train (the Palmetto, #90), has left SAV on time almost every day for the last month, and arrived at CHS with a median delay of only 3 minutes over the same time period. The evening train (the Silver Meteor #98) has a rather worse record, with a median departure delay of 38 minutes and a median arrival delay of 51 minutes; 20 of 30 were more than half an hour late. Again, however, I'd much rather spend an extra hour on Amtrak than an extra fifteen minutes on, say, Spirit Airlines.

While Amtrak in some cities is ideal for traveling downtown to downtown, convenience is not a strong selling point here. The stations are about four miles and nine miles from Savannah and Charleston's respective city markets. This may be why people recommend the Basin Bus for tourists, since it goes from tourist district to tourist district directly. Savannah's Greyhound terminal is also located in the downtown area, although Charleston's is still a taxi ride away.

Amtrak will rank among the preferred transportation options within the Northeast, and especially between the major cities along the Northeast Corridor. Other than a handful of intra-state corridor routes, it does not come close to that mark anywhere else in the country. This is not necessarily because most people have bad experiences with Amtrak, but because most people do not have any experience with Amtrak at all. Intercity rail is not practical for most people for most travel at most times in most of the United States. Many Americans are unaware service is available in a particular locale, or forget that Amtrak even exists.

There is extensive commentary on the historical and economic reasons for the decline of passenger railroads in the U.S.—too much to get into on TSE—and the matter is extremely fraught politically. For now, there is enough political will to subsidize Amtrak enough to keep it going, but not enough either fund it to the point where it could thrive or to cut it off entirely. I leave it to you to research the root causes on your own.

In practical, retail-level terms, Amtrak is not a viable for many travelers in many parts of the country for reasons that include one or more of the following:

• Frequency. Many cities are served by only one or two trains in each direction per day. There is no service at all even to some large cities, like Columbus, Ohio or Nashville, Tennessee, each with a metro area population of around 2 million people. Even between Washington, D.C. and Chicago, there is only a single daily direct train in each direction, while United Airlines currently sells no fewer than 22 nonstops.
• Schedule. As a corollary to the limited frequency, departure and arrival times will be impractical for many. That Washington-Pittsburgh service (the Capitol Limited) departs Washington at 16:05 and arrives in Pittsburgh at 23:48. The return departs at 05:20 and arrives 13:05. That makes it impractical for a business trip or even a weekend family visit to Pittsburgh considering I can drive there in four hours or fly there in about one hour. Why doesn't Amtrak schedule more trips? In many cases, they would, to meet demand, but Amtrak does not have any extra trains, nor the capital to purchase them, and many rail lines are being run at capacity anyway
• Reliability. Every mode of transportation can see delays and irregular operations, of course, but it is a much bigger ordeal to reroute a train to avoid, say, flooded track, than it is to reroute a bus or a plane. Although Amtrak trains have priority over freight trains, they still have to share the tracks, and you can get stuck behind a freight train on many services. In the Northeast in particular, you have issues with aging infrastructure
• Speed. I can drive from Washington to Pittsburgh in four hours; the most direct Amtrak service takes more than seven and a half. Of course, on other routes, you may save a lot of time avoiding traffic, besides the cost of parking and fuel and of course the rental itself, but there is a tipping point for each city pair. Add to this that many train stations are located outside city centers, so may not be any more convenient than a small airport.
• Cost. Coach seats on long-distance trains can be relatively inexpensive, as you've found. On other routes, it's impractical compared to driving or flying. It's quite expensive along the NEC, but even on inexpensive routes, the fares add up, especially for groups. Two people can drive from Los Angeles to San Diego in about three hours for under $10 per person in gasoline. They could instead take Amtrak's Pacific Surfliner, which is a generally fantastic ride, and take roughly the same amount of time, but it would cost $35 each.
• Competition. The domestic air and road network in the U.S. is well-developed. September 11 was an outsized economic shock in part because at the time, half of all air travel in the world (measured by revenue passenger kilometers) was within the United States. Consider that nowadays, from Washington to New York, you can take a bus that takes about 4½ hours and costs $19; you can take Amtrak, which takes 3½ hours and costs $80; or you can take the Delta Shuttle, which costs $100 and takes about one hour. Mind you, this is one of the routes where it makes the most sense to take Amtrak in terms of other practicalities, but it remains that if you want to save money, you'd take the bus, and if you want to save time, you'd fly.
• Unfamiliarity. You don't recommend what you can't vouch for, and at this point in our history, a distinct minority of people have taken Amtrak or its predecessors. That, again, is a trend that started decades ago and accelerated greatly with jet aircraft and interstate highways. When I moved to the East Coast and started taking the train, at least a few of my West Coast friends said it was "weird."