You have to compare apples and apples.

Top of the line Trek Madone has an MSRP of $8249. I buy it locally, add 7% sales tax, I'm going out the door for $8826.

A fully custom Calfee Dragonfly will set you back $3500 for the frame and fork. Add $3800 to get it built ($1500 for DA10, $1500 for wheels, $800 for the other pieces). Now you're riding a bike that was built precisely for your needs (yes, even if you would fit perfectly on a stock whatever) and one with a paint job that is your own personal choice. A one off, the only bike in the world like it and you just saved $1500 in getting it.

Don't like Calfee? How about a Crumpton, generally recognized as the top custom carbon fiber builder in the country. At least among his peers. $4800 for the frame, plus $3800 for the goods and you've still saved a couple of hundred dollars.

And if you fall into the camp of "materials don't really matter", you can build yourself an outrageously well appointed steel bike for less than $5000.

At the lower end, sure, you can get a darn nice bike at the LBS for $2000 and you'll be hard pressed to beat that price with custom. You can come close though, even at that price break. A fully custom steel Gunnar will run you $1275 with a CF fork. Built with Ultegra or Centaur, $2300 to $2500.

It all depends on what compromises you're willing to make - looks, exposed seat post, components - if these things don't matter to you, and if you're not willing to invest the time to shop and work with a builder, then straight retail is the way to go.