i find for problems with circuits the 3 most common problems you will see are 1. power, 2. short circuits and 3. a dumb typo somewhere.
1. test the voltage between the microcontroller's VCC and GND pins with a multimeter to make sure there is no problem with the microcontroller's power.
2. if power looks ok check each of the connections between your programmer pins and the microcontroller pin it is connected to. test the resistance with a multimeter between each pin and any of it's neighbours it might be mistakenly touching.
you should get no resistance between points in the circuit that are connected and very high resistance between unconnected pins.
3. leave it alone for a day. try to come back with a fresh set of eyes and see where you might have connected the wrong thing to what... sometimes we all do something wrong and can't see it.
as long as you can satisfy your self that the microcontroller is powered correctly and that the programmer pins are connected to the correct microcontroller pins then i think you are safe to say the problem you are experiencing is not with the circuit but rather with your PC side software setup.
for a home made programmer i use this: http://www.instructables.com/id/Ghetto-Programming:-Getting-started-with-AVR-micro/