It would seem to me that Trek has a model that works for the average LBS owner. Is that Trek's fault? Nope.
I think the bigger question is why doesn't other bike manufactuers copy Trek in this standpoint? If Trek is cornering the market in terms on being on 90% of LBS's sales floors... Well, it seems to me they are doing something right.
As far as Bontrager goes. Why the hate? I freely admit I have a Madone 5.9 with Bontrager components on it and they work fine. Acutally, more than fine. The new 08 X-Lite wheels might be the best wheels I have ever ridden on. That includes a set of DT Swiss.
In the end, they have a great model of delivering their bikes to the public and the other manufacturers need to catch up.