The only downside is almost none of these systems are in operation 24/7, with the exceptions being NYC and Chicago. If you have a very early or late arrival / departure, you just can't use them at all without waiting several hours at the airport. I wish more cities could add reduced frequency night service, something like maybe 1 train every hour or hour and a half.
As a somewhat cherry-picked example, if someone in the southern part of my city wants to take a train into the city center, the last good route with only one transfer leaves at 10 pm. At 10:40pm Google maps suggests a route with 3 transfers that takes almost twice as long (and includes the commuter rail which is a separate, more expensive ticket). The last possible option is at 11:40 and takes 3 times as long as the normal route. If we want people to use trains and subways, the service hours have to be greatly improved.