First, check to make sure the rotor is dead straight. If there's a particular strike spot (a la *CHING* *CHING* *CHING* as the wheel turns, it might be slightly bent. There's a special tool to bend a hop back, but you can even do it with your hand or an adjustable wrench.
If that's not the cause, remove the wheel and take out the brake pads. Use a flathead screwdriver to manually push the pistons back (inside the caliper). If you change your brake pads and don't do this, the hydraulic fluid keeps the pistons where they where, which closes in on your rotor with a set of new pads in place. It will take a little force, but you should be able to get them to retract (same basic concept as a car).
Once the pistons are pushed back, put the pads back on and the wheel back on. Park Tool has a handy shim guide for disc brakes, but you can make do with a thin piece of aluminum (like .024 or .040 gauge max). Slide these shims between each of the pads and the rotors and pump the brakes to recalibrate the pistons. You want to get things tight with the shims in place. Remove those shims, and that should provide the proper clearance for good reacting brakes without any rubbing issues.
Hope this helps.