I can tell you that I bought a Cannondale hybrid for "commuting", in my price range (about $500) and soon after, realized that I should have gone with a road bike. My commuting needs took a backseat to the type of riding I really wanted to do - hard, fast, and long. I ended up getting a Blue RD1 after less than a year of ownership with my hybrid... it probably had less than 100 miles on it.

So, I can understand what the LBS are telling you about not leaning towards "entry level" bikes. But what are your needs? Simply commuting may be a hybrid, or even a cyclocross... but if you're wanting something more, you may want to shop around. If you're wanting something in the sub $1K category, componentry is going to be BASICALLY the same all around, so, to echo everyone, the FIT is genuinely the most important. Go with what feels the best for you - your body will thank you later.