The market is just not there in Jakarta to fill up al of those wide-body seats, so airlines are using Singapore's liberal policies to serve Jakarta as a tag on to their Singapore flights, thereby entering the very busy Jakarta-Singapore traffic. Some airlines on the route include:
Quite a few airlines use Kuala Lumpur as a stopover point as well:
KLM (from October)
Royal Jordanian (temporarily suspended)
For Garuda Indonesia, Singapore can be considered a hub as it transfers passengers from its longhaul/international network to various points in Indonesia at Singapore. On the international side, Garuda serves Amsterdam, Shanghai, Hongkong, Bangkok and Ho Chi Minh via Singapore, while these flights connect into flights to Medan, Pekanbaru, Padang, Jakarta, Semarang, Jogjakarta, Surabaya and Denpasar at Singapore.