hmmm thats a good question.
I believe both recommended AVR programmers have a built in protection circuit (especially the more expensive Atmel one) . . . but I could also be wrong . . . does someone know for sure?
Worst case scenario you will only end up damaging your serial port.
If you are using a serial to USB converter, it is almost guaranteed to have a safety buffer built in.
Anyway, before plugging in your circuit to your PC, you should always use a multimeter to make sure all the pins are doing what they are supposed to do.