After making sure your brakes are all in proper working condition, AND checking/adjusting the E-brake, if it STILL does it, and you cant find any thing obvious, check the sensor on the side of the reservoir. The intermittent "flashing", and short duration of the light coming on, usually only while in motion, and especially hitting bumps, going around corners, or up down slopes, is a good indication its probably the sensor.
I had this problem with my 99 Taco. Checked everything, and it turned out to be a bad float switch on the side of the brake reservoir. It is what triggers the idiot light when the fluid level in the reservoir gets low. IIRC, a new one was pretty pricey, and I didnt feel like spending the money at the time, so I just ran it unplugged...No more annoying idiot light. You just have to make sure you check your brakes and fluid more often, as well as remembering to dis-engage your E-brake. (I often forgot that part, and the idiot light was no help, as who really looks at all their ID-Ten-Tee lights before taking off after startup, anyway...??)