In My opinion it is around 3-5%. I recently read in a newspaper that the margin is not much for the dealers to survive. So the dealers were asking for an increase in the margin for sustainability.
When I purchased my TATA SAFARI in 2007, the dealer margin was 34k. I could get it as the ex-factory price shipping insurance invoice that came along with the registration forms where the price was mentioned and the ex-showroom price difference that I calculated made me arrive at the margin.
Dealers make more money by cashing in on Temp registration amount, which incidentally in Hyderabad is only 200 and is paid online at the dealer login id itself after entering all the details into the RTA portal. But these showroom guys charge us 2k for it.
Similarly while purchasing our Scorpio, I noted that many accessories go into the car, like the central AC panel, DVD, chrome accents, etc., in a pack worth 2,76k on MRP is given at 2,35k.
But central AC panel, mud flaps, carpets, etc., in a smaller or basic pack come at 33-35k which is all dealers margin. They make a killing here. But again all these are not covered in the warranty and any mishap is void of warranty.
What about handling charges. They are actually not supposed to be charged at all. Again insurance. Many of us know that outside it is cheaper, but many items we are forced to take it with the dealer.
So these all add to the dealers margin.
Edit:
Just found a link. 2013 Business line says it is usually around 2.5%, but highest is by TATA MOTORS at 4%.
dealer demand increase in margins