Okay, let's do this step-by-step.
One, the Bajrang Dal, the VHP and the Hindutva loonies are largely funded by India's trading class.
Two, the Hurriyat is funded by Pakistan but it's leaders take money from R&AW from time to time.
Three, the Centre takes the view that it is better to have the Hurriyat in full public view than to drive it underground and allow its supporters to drift into terrorism.
Four, I don't think the Hindutva loonies are funded very differently from normal political parties so it is difficult to take selective action against them.