It is annoying and it makes no sense for them to take it out on the passenger but understand that in a lot of places one short distance fare can make the difference between making money and losing money in a day. They get a double whammy too because not only do they have to go back into line but also there's little chance they will get a fare back to the airport from close in.

The EWR system seems reasonable as it tries to solve the problem but does not punish the passenger. They have (or had, it's been a while) a system at ORD too where there were different cab stands for different destinations but I never really figured this out.