A pulsing or vibrating brake pedal is most often a symptom that your rotors are warped. It can also be an indicator that the vehicle itself is out of alignment. If your Honda has an anti-lock braking system, the vibration can feel quite similar to what is felt in the brake pedal during an emergency stop.
If the vibration is occurring during braking without engagement of the anti-lock brakes, this is a sign that the rotors have been warped. Warped rotors are most commonly caused by braking severely for long periods of time, like when driving down a mountains or hills that are steep, or when towing another vehicle. An enormous amount of friction is created when these conditions occur, making the rotors heat up and causing warping. The vibration can be felt since the brake pads are unable to evenly grab the surface. If you must drive in conditions like these, be sure to make periodic stops so that the brakes can cool off.