Assuming(!) that your braking system is in good working order, then the 'soft' feeling brakes could very well be normal. Scroll down to 'New Features and Options for 2003 models', sixth item on the list:
I can feel a noticeable difference in pedal effort between my '00 WJ and my wife's '03. I do find it a bit disconcerting that I can apply the pedal almost all the way to floor on her '03, however driving the two back to back, I do feel that the '03 brake system provides a more linear feel in braking, while my '00 almost feels on/off when applying the brakes.
I think what bothers most people is that our instinct tells us the hard we push the pedal, the more resistance we should feel. In the case of '03+ WJ's, the harder you push the farther the pedal travels to the floor.