There are one of two, or maybe two, problems. The one I would look at first would be the master cylinder, because even if the caliper is frozen the master cylinder should be able to push the piston out! I would buy a master cylinder rebuild kit which will cost you about $40-45. Honda p/n 43520-MJ6-305. The other thing you should do is remove the caliper from the bike and take the piston out and check them for wear and replace the seals and dust seals in the calipers if needed. The seals can be bought in a set for about $5. Honda p/n06431-MA3-405. If the piston is shot it will run you around $20-25, but I doubt that is bad unless you've had a lot of gunk in your brake system. The best way that I know of to get the piston out of the rear caliper, if the brake system will not push it out by just adding brake fluid to the system and pumping the pedal till it pops out (with the caliper removed and the pads removed), is to take the caliper completely off the swingarm and rotor and disconnect the brake line and push the piston out with air pressure from a compressor. You will need a air gun, parts cleaner type of deal with the rubber nozzle on it. You put a heavy towel over the piston and hold it with your hand and blow high pressure air from a compressor into the hole that the bolt that holds the brake line on came out of. Be very careful when doing this to somehow contain the brake piston, as it can become a projectile which will easily penetrate sheetrock/glass/other stuff you don't want broken. Once you get the piston out, remove the seal, and clean the grooves they came out of with break fluid and an old tooth brush. It is common to get some white mold type of stuff behind the seals. Clean the piston up with the same toothbrush and brake fluid, put the new seals into the caliper and rub a little fresh brake fluid on them and push the piston back into the caliper. Rebuild your master cylinder, this is pretty self explanatory, you just put it back together the way you took it apart. Keep an eye out for the white stuff I told you about earlier. If you decide to do this you should probably get some new copper washers at the same time you order your other stuff so you don't get everything done and then have it leak when you put it all together. The washers are honda p/n90545-300-000 and you'll need 4 of them, about $2. Oops, I almost forgot, make sure to flush the rear caliper out when you have the piston out to clear any foriegn material that may have worked it's way into the system. Don't forget to use some anti-sieze compound on your break pins when you put the pads back in so you don't have a headache down the road when you need to change the pads next and the pins are frozen into the caliper.
Good luck, it's not really that hard, it just helps to know what to do.