The shortest and clearest answer to the question posed in the title is “Nobody knows.” To call the politics of South Asia “murky” is the understatement of the century.
The mainstream of opinion seems to prefer the theory that they were militant Islamists. Animesh Roul over at Counterterrorism Blog posits that they may have been Kashmiri militants (specifically  Lashkar-e-Toiba) impersonating homegrown Indian jihadis (hence the “Deccan Mujahideen”, a group nobody had ever heard of, claiming responsibility).
However, there are others who believe that they were actually militant Hindus impersonating Islamists and therefore …