This isn't the complete answer to a very complex issue, but until new pads are fully bedded into the rotors the pedal will be noticably softer than before. This is a very common complaint when brake pads are replaced, especially if the rotors are not machined at the same time.
Beyond that, the most common cause of a soft pedal is air in the system or old fluid. Fresh fluid with old but still excellent pads often feels noticably firmer.
The pedal can also be soft from a worn master cylinder, but this is quite uncommon.
