I took the late evening train from Jogja to Jakarta. The travel distance is lesser than the distance between Madurai and Chennai. Though the executive class is quite comfortable (like the 1st class), the commute time is high. So, if you intend to catch an early morning flight at Jakarta (before 8 AM), then it could be quite a gamble. To my luck the train was late by an hour and a half. I could luckily get the airport shuttle from the Gambhir Station.The shuttle runs every 15 mins and it shouldn’t be an issue. Allow another 45 to 1 hr 20 mins to reach the airport. The shuttle has to go thru toll booths on expressway. As of 1st March 2009, Soekarno-Hatta Airport charges IDR 150000 as departure tax for international flights.
P.S: Kereta Api means train in Bahasa Indonesia.