Bzzzzt incorrect or errr ummmm DISAGREE! You LBS salesman is just that.... a salesman.

The comfort in a frame is not in the material. It is in the geometry of the frame and the tube profiles that are incorporated into it. You can easily get an ultra stiff kidney wrecking frame from carbon, just as you can get a soft supple riding frame from aluminium and vice versa. Aluminium is not often used for the purpose due to the weight concerns of new bike purchasers these days and the fatigue life assosciated with the material.

The ride of different tyres is the thing that a lot of people don't give enough props to, along with wheel types. If you are chasing a new bike, you should really ride each bike with the same wheel/tyre combo to effectively discern which rides better than the other. Small changes in PSI, tyre width and wheels can massively affect the way a bike rides.