I was just chatting with the long-time owner of a high-end LBS near me. He commented on the demise of indy bike shops, and specifically mentioned Trek buying out shops and replacing employees. On the other hand, another nearby indy shop is very loyal to Trek- they had a fire a few years back, losing a big inventory, and Trek took care of them.
I've visited a couple of Trek stores, and yeah, much more of a department store, big box vibe. I stopped in one outside Cincinnati, I was impressed they had a good selection including the (then) new aero Madone 9.9