It is not uncommon to have a mushy brake pedal after doing a brake job. What typically occurs is that the air gets trapped in the lines during the piston push-back process. In most cases this mushy feel will go away with time but in extreme cases you may have to bleed the brake calipers at each wheel to get the air out.
NOTE: Most brake jobs require a break-in period after doing a brake job which will allow the need pads to seat to the new (or old) rotors. This can take from one week to two weeks.
Thanks to Justin Campbell-Gillies for contributing to this FAQ!
I just replaced my brakes and had a soft pedal with a long travel before the brakes would start to grab. The mistake I made was putting the springs on the front caliper on incorrectly. They were pushing the caliper away from the hub instead of pulling it inward. This meant that the piston was being pushed back every time I let off the brakes and therefore it had to travel further to engage. A few minutes work putting them on correctly and all was well again.