Again, it needs your bargain skills. For example, it is about Rp 5.000 to ride from stasiun Tugu along those Jalan Malioboro.
Beside aeroplane, Jogja can be reach easily using train. Choose Argo Lawu or Turangga from Jakarta to destination Jogjakarta, Tugu railway station. Approximately per person Rp. 130,000,-