Cabell - I think it comes down to a question of land cost and debt service. You'll discover that most of the architecturally significant courses charging the type of fees you describe happen to be located in areas where land costs are nearly prohibitive, or, at the very least, near large population centers. Examples of this would obviously have to include Friars Head, Sebonack, Boston, Nantucket, etc.
On the other hand, I think you'll find that a number of the really significant courses that don't charge the type of fees you cite are located in areas where land costs are more reasonable, e.g. Sand Hills, Kingsley, etc.
I'm really not sure there is much that can be done about it save finding a group of investors who are willing to bleed it out.