If your brake fluid is low, and you don't have any fluid leaks, then you need to check your brake linings for wear. Chances are they are worn thin. When you replace them, the fluid will push back up from the calipers and/or wheel cylinders into the master cylinder. In other words, the fluid that WAS in your master cylinder is down in the calipers or wheel cylinders now.... unless it leaked out.

 

+1, and if you do replace your pads, get a turkey baster or something and remove some fluid from the reservoir before you compress the brake caliper pistons (since you just topped off). Not a big deal, but if you don't do so, you will get a mess of brake fluid overflowing from the master cylinder, down on to the frame and floor.