Take a look at the space between the pads mounted in the caliper and the rotor and you will find that you are dealing with a very narrow gap. It is important to reallize this as you can push/pull/bend your rotor all day long and not fix the rubbing problem until you reallize the resolution you need to be pursuing.

When truing the rotor start by flexing the arms of the spider holding the outer diameter of the rotor to the center of the rotor. Finer tuning of the rotor may require flexing single small segments of the outer portion that runs through the brake pads. Use an adjustable wrench or tool specific to this task (Park makes one). There is a company that sells the tool in a pack of 3 where two tools are used to stabalize the rotor and a third placed in the middle of the other two is used to bend the disk...This system works well in theory but in reality I have found using this system to be a pain and more trouble than its worth compared to using a single tool on the rotor. I use a park ts-2 with their rotor truing guage and a dial caliper at my home shop.

Once you know that your rotor is straight do the following:
1. Mount your wheel properly in your frame.
2. Loosen the bolts holding your caliper to the frame adapter or to the frame if there is no adapter. You want the caliper to be able to float around on the bolts.
3. Spin your wheel.
4. Grab your brake lever and hold it firmly while you tighten the caliper bolts.
5. Keep an eye on the caliper while tightening the bolts to ensure it does not creep when tightening the bolts.
6. Your caliper should now be centered on your rotor. If not, sight down between the pads and the rotor to see which pad is rubbing and whether it is the top or bottom portion of the pad that is rubbing the rorot. Loosen the caliper bolt closest to the portion of the pad that is rubbing and apply a little pressure against the side of the caliper to creat the gap needed and then tighten the caliper bolt. Now your caliper should be centered without rubbing.

Hydraulic disk brakes generally work reallly well but can be frustrating to dial in. I normally only ride with a tube, pump, and tire levers, but since obtaining a mt bike with hydraulic brakes I keep 5mm allen wrench in my saddle pouch to facilitate centering my calipers if I have to pull a wheel for any reason.

-j