I would take the train from JAX to Miami over driving ANY DAY. One slight problem though, once a passenger gets off in either JAX of Miami, they're kind of stranded. See, unlike Penn Station NYC, Newark, or Union Station Philly, neither JAX nor Miami really have the local mass transportation connectivity that the previously mentioned cities do.
Don't get me wrong, I think that this connection is a step in the right direction, but I'm just think about the next level, local mass transportation.