There are still costs involved from the automakers down to the private sellers. Excess dealers competing for the same business brings down the retail market costing lots of sales among dealers, and with fewer buyers these days thats results in the automaker having dealers fighting over the same sales more and more, not healthy for anyone in the industry but the buyer.
Another thing is that I think is killing them but this is just my opinion is some of the dealers themselves. With all the struggling dealers out there they have less money for PROPER advertising, modern buildings that attract customers, customer amenities, etc. that leads to a strong sales line within the brand. Dealers are having to sell their inventory at huge losses, not giving them the revenue to keep up with other large productive dealers who are more high volume and can afford to take a bigger hit on vehicles because they are moving more inventory.
As for costs that the autmaker has with dealers, they pay for administrative services, marketing assistance, parts and service support, auditing, etc. One site I was reading last night said that they are spending almost $500 more on a Detroit vehicle than national average, which was costing them almost $3-4 billion, would have to double check that.
Ya it sucks, even in my hometown here in Bismarck, ND, we have one of the oldest family owned Dodge/Chrysler dealers in the US and they will be closing their doors to the brand name. But I would also have to say they saw it coming as they just built a new store based on the Toyota brand they carry, and said the Dodge/Chrylser portion was only 25% of what they do now. Another one is we have 3 GM dealers here in town, 3 for the size of less than 80,000. That is way to many in my mind, as you can already see here that the Pontiac dealer was struggling and the two Chevrolet dealers aren't even close by comparison. One dealer is already making most of the sales here as they have been doing things right for a long time, you can see the other two struggling for years to keep up in the market here, it is just not healthy as a whole.
Sorry for being long winded, just my .02